Mercurial > repos > siwaa > erecord_file

annotate erecord_file.xml @ 3:aa5c088856c8 draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 490623122691651ac91c33d75ea1898189be7512-dirty
author siwaa
date Thu, 15 Feb 2024 15:24:53 +0000
parents 9e8f5f220917
children
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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
siwaa
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1 <tool id="erecord_file" name="erecord_file" version="1.0.0">
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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3 <description>erecord returning .json + maybe .zip or .xls</description>
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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5 <requirements>
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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7 <!-- singularity -->
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8 <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/erecord-deploy/rep_recordb:9d6ea1defd50dd63fe036a7545a9ea527572192e</container>
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
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9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
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10 <!-- image locale -->
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
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11 <!-- container type="singularity">/home/nrousse/workspace_git/SIWAA_regroup/erecord-deploy/containers/_fab_SIMG/rep_recordb.simg</container-->
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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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13 </requirements>
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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15 <command detect_errors="aggressive">
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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16 <![CDATA[
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17 . /PYVENV/bin/activate;
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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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19 echo "action_name VAUT $request_condition.action_name";
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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20 #if $request_condition.action_name == 'post_vpz_experiment':
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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21 /bin/bash -c "python3 $__tool_directory__/main_file.py -action ${request_condition.action_name} -data ${input_json} -datafolder ${datafolder} -experimentfile ${experimentfile}";
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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22 #elif $request_condition.action_name == 'post_vpz_report':
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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23 /bin/bash -c "python3 $__tool_directory__/main_file.py -action ${request_condition.action_name} -data ${input_json} -datafolder ${datafolder}";
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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24 #elif $request_condition.action_name == 'post_vpz_output':
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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25 /bin/bash -c "python3 $__tool_directory__/main_file.py -action ${request_condition.action_name} -data ${input_json} -datafolder ${datafolder}";
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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26 #elif $request_condition.action_name == 'post_vpz_inout':
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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27 /bin/bash -c "python3 $__tool_directory__/main_file.py -action ${request_condition.action_name} -data ${input_json} -datafolder ${datafolder}";
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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28 #else:
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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29 /bin/bash -c "python3 $__tool_directory__/main_file.py -action ${request_condition.action_name} -data ${input_json}";
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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30 #end if
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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32 cp WS/OUT/output.json ${output_json};
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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34 #if $request_condition.action_name == 'get_vpz_experiment':
2
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
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35 touch WS/OUT/experiment.xls;
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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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36 cp WS/OUT/experiment.xls ${experiment};
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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37 #elif $request_condition.action_name == 'post_vpz_experiment':
2
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
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38 touch WS/OUT/experiment.xls;
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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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39 cp WS/OUT/experiment.xls ${experiment};
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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40 #elif $request_condition.action_name == 'get_vpz_report_conditions':
2
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
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41 touch WS/OUT/conditions.xls;
0
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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42 cp WS/OUT/conditions.xls ${conditions};
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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43 #elif $request_condition.action_name == 'post_vpz_report_conditions':
2
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
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44 touch WS/OUT/conditions.xls;
0
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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45 cp WS/OUT/conditions.xls ${conditions};
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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46 #elif $request_condition.action_name == 'get_vpz_report':
2
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
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47 touch WS/OUT/report.zip;
0
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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48 cp WS/OUT/report.zip ${report};
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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49 #elif $request_condition.action_name == 'post_vpz_report':
2
9e8f5f220917 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 2bd91617d46a1c454a7a167113cc605bdd1b3ff2-dirty
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50 touch WS/OUT/report.zip;
0
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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51 cp WS/OUT/report.zip ${report};
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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52 #end if
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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53
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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54 ]]>
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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55 </command>
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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57 <inputs>
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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58
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59 <param name="input_json" optional="true" type="data" format="json"
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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60 label="Input json file"/>
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61
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62 <conditional name="request_condition">
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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63
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64 <param name="action_name" type="select" label="Select action">
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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65 <option value="help" selected="true">help</option>
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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66 <option value="get_pkg_list">get_pkg_list</option>
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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67 <option value="get_pkg_vpz_list">get_pkg_vpz_list</option>
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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68 <option value="get_pkg_data_list">get_pkg_data_list</option>
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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69 <option value="get_vpz_input">get_vpz_input</option>
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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70 <option value="post_vpz_input">post_vpz_input</option>
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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71 <option value="get_vpz_output">get_vpz_output</option>
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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72 <option value="post_vpz_output">post_vpz_output</option>
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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73 <option value="get_vpz_inout">get_vpz_inout</option>
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74 <option value="post_vpz_inout">post_vpz_inout</option>
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75 <option value="get_vpz_experiment">get_vpz_experiment</option>
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76 <option value="post_vpz_experiment">post_vpz_experiment</option>
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77 <option value="get_vpz_report">get_vpz_report</option>
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78 <option value="post_vpz_report">post_vpz_report</option>
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79 <option value="get_vpz_report_conditions">get_vpz_report_conditions</option>
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80 <option value="post_vpz_report_conditions">post_vpz_report_conditions</option>
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81 </param>
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82
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83 <when value="post_vpz_experiment">
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84
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85 <param name="experimentfile" type="data" format="csv,xls"
27e7e4d38e44 planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
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86 label="Add a experiment xls (csv) file"
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87 help="experimentfile from gest_vpz_experiment + modifications"/>
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88 <param name="datafolder" optional="true" type="data" format="zip"
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89 label="Add a datafolder zip file"
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90 help="Precisions sur forme du dossier..."/>
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91 </when>
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92
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93 <when value="post_vpz_report">
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94 <param name="datafolder" optional="true" type="data" format="zip"
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95 label="Add a datafolder zip file"
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96 help="Precisions sur forme du dossier..."/>
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97 </when>
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98 <when value="post_vpz_output">
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99 <param name="datafolder" optional="true" type="data" format="zip"
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100 label="Add a datafolder zip file"
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101 help="Precisions sur forme du dossier..."/>
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102 </when>
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103 <when value="post_vpz_inout">
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104 <param name="datafolder" optional="true" type="data" format="zip"
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105 label="Add a datafolder zip file"
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106 help="Precisions sur forme du dossier..."/>
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107 </when>
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108
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109 <when value="get_vpz_experiment" />
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110 <when value="get_vpz_report_conditions" />
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111 <when value="post_vpz_report_conditions"/>
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112 <when value="get_vpz_report" />
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113 <when value="get_vpz_input" />
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114 <when value="post_vpz_input" />
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115 <when value="get_vpz_output" />
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116 <when value="get_vpz_inout" />
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117 <when value="get_pkg_list" />
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118 <when value="get_pkg_vpz_list" />
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119 <when value="get_pkg_data_list" />
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120 <when value="help" />
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121
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122 </conditional>
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123
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124 </inputs>
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125
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126 <outputs>
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127
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128 <data name="output_json" format="json" label="output_json"/>
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129
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130 <data name="experiment" format="xls" label="experiment">
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131 <filter>request_condition['action_name'] == 'get_vpz_experiment' or request_condition['action_name'] == 'post_vpz_experiment'</filter>
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132 </data>
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133
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134 <data name="conditions" format="xls" label="conditions.xls file">
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135 <filter>request_condition['action_name'] == 'get_vpz_report_conditions' or request_condition['action_name'] == 'post_vpz_report_conditions'</filter>
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136 </data>
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137
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138 <data name="report" format="zip" label="report">
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139 <filter>request_condition['action_name'] == 'get_vpz_report' or request_condition['action_name'] == 'post_vpz_report'</filter>
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140 </data>
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141
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142 </outputs>
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143
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144 <tests>
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145 </tests>
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146
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147 <help><![CDATA[
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148
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149 erecord_file.xml
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150
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151 ================
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153 Actions:
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155 -------
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157 - 'help'
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158 - 'get_pkg_list' 'get_pkg_vpz_list' 'get_pkg_data_list'
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159 - 'get_vpz_input' 'post_vpz_input'
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160 - 'get_vpz_output' 'post_vpz_output'
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161 - 'get_vpz_inout' 'post_vpz_inout'
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162 - 'get_vpz_experiment' 'post_vpz_experiment'
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163 - 'get_vpz_report_conditions' 'post_vpz_report_conditions'
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164 - 'get_vpz_report' 'post_vpz_report'
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165
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166 Code:
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167
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168 ----
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169
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170 - main_file.py
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172 Inputs:
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173
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174 -------
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175
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176 - action value (mandatory)
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177
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178 - data json file (optional) (json file, param type="data")
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179 An action value that would be into data would be ignored
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180
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181 - experiment.xls (only in 'post_vpz_experiment' case)
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182
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183 - datafolder (optional) (only in cases :
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184 'post_vpz_experiment', 'post_vpz_report', 'post_vpz_output', 'post_vpz_inout')
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185
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186 Outputs:
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187
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188 --------
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189
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190 - data json file
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191
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192 - 1 other file (xls or zip) :
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193 - if 'action' == get_vpz_experiment, post_vpz_experiment :
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194 experiment.xls file
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195 - if 'action' == get_vpz_report_conditions, post_vpz_report_conditions :
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196 conditions.xls file
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197 - if 'action' == get_vpz_report, post_vpz_report :
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198 report.zip file
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199
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200 Credits:
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201
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202 --------
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203
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204 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
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205 - Copyright: INRAE
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206
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207 ]]>
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208 </help>
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209
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210 </tool>
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211