Mercurial > repos > siwaa > erecord_file

annotate erecord_file.xml @ 0:27e7e4d38e44 draft

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planemo upload for repository https://forgemia.inra.fr/nathalie.rousse/erecord-deploy/-/tree/main/galaxy-tools/erecord_file commit 88beb443a737b4c4d42bb0011a26a0acf535c366
author siwaa
date Tue, 12 Dec 2023 17:33:05 +0000
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children 9f7e56f56079
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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 -->
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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8 <container type="singularity">oras://registry.forgemia.inra.fr/nathalie.rousse/erecord-deploy/erecord_rep0_vle2:82d8fea607be20851e194828125785fb0f7e96d0</container>
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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10 </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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12 <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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13 <![CDATA[
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 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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16 #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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17 /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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18 #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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19 /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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20 #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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21 /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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22 #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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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
siwaa
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24 #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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25 /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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26 #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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27
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 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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30 #if $request_condition.action_name == 'get_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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31 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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32 #elif $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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33 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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34 #elif $request_condition.action_name == 'get_vpz_report_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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35 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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36 #elif $request_condition.action_name == 'post_vpz_report_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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37 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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38 #elif $request_condition.action_name == 'get_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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39 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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40 #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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41 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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42 #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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43
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44 ]]>
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45 </command>
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46
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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47 <inputs>
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48
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49 <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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50 label="Input json file"/>
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51
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52 <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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53
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54 <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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55 <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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56 <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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57 <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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58 <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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59 <option value="get_vpz_input">get_vpz_input</option>
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60 <option value="post_vpz_input">post_vpz_input</option>
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61 <option value="get_vpz_output">get_vpz_output</option>
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62 <option value="post_vpz_output">post_vpz_output</option>
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63 <option value="get_vpz_inout">get_vpz_inout</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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64 <option value="post_vpz_inout">post_vpz_inout</option>
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65 <option value="get_vpz_experiment">get_vpz_experiment</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="post_vpz_experiment">post_vpz_experiment</option>
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67 <option value="get_vpz_report">get_vpz_report</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="post_vpz_report">post_vpz_report</option>
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69 <option value="get_vpz_report_conditions">get_vpz_report_conditions</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_report_conditions">post_vpz_report_conditions</option>
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71 </param>
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72
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 <when value="post_vpz_experiment">
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74
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75 <param name="experimentfile" type="data" format="csv,xls"
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76 label="Add a experiment xls (csv) file"
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77 help="experimentfile from gest_vpz_experiment + modifications"/>
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78 <param name="datafolder" optional="true" type="data" format="zip"
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79 label="Add a datafolder zip file"
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80 help="Precisions sur forme du dossier..."/>
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81 </when>
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82
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83 <when value="post_vpz_report">
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84 <param name="datafolder" optional="true" type="data" format="zip"
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85 label="Add a datafolder zip file"
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86 help="Precisions sur forme du dossier..."/>
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87 </when>
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88 <when value="post_vpz_output">
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89 <param name="datafolder" optional="true" type="data" format="zip"
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90 label="Add a datafolder zip file"
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91 help="Precisions sur forme du dossier..."/>
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92 </when>
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93 <when value="post_vpz_inout">
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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
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99 <when value="get_vpz_experiment" />
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100 <when value="get_vpz_report_conditions" />
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101 <when value="post_vpz_report_conditions"/>
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102 <when value="get_vpz_report" />
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103 <when value="get_vpz_input" />
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104 <when value="post_vpz_input" />
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105 <when value="get_vpz_output" />
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106 <when value="get_vpz_inout" />
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107 <when value="get_pkg_list" />
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108 <when value="get_pkg_vpz_list" />
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109 <when value="get_pkg_data_list" />
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110 <when value="help" />
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111
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112 </conditional>
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113
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114 </inputs>
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115
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116 <outputs>
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117
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118 <data name="output_json" format="json" label="output_json"/>
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119
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120 <data name="experiment" format="xls" label="experiment">
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121 <filter>request_condition['action_name'] == 'get_vpz_experiment' or request_condition['action_name'] == 'post_vpz_experiment'</filter>
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122 </data>
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123
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124 <data name="conditions" format="xls" label="conditions.xls file">
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125 <filter>request_condition['action_name'] == 'get_vpz_report_conditions' or request_condition['action_name'] == 'post_vpz_report_conditions'</filter>
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126 </data>
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127
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128 <data name="report" format="zip" label="report">
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129 <filter>request_condition['action_name'] == 'get_vpz_report' or request_condition['action_name'] == 'post_vpz_report'</filter>
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130 </data>
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131
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132 </outputs>
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133
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134 <tests>
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135 </tests>
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136
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137 <help><![CDATA[
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138
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139 erecord_file.xml
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140
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141 ================
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142
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143 Actions:
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144
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145 -------
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146
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147 - 'help'
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148 - 'get_pkg_list' 'get_pkg_vpz_list' 'get_pkg_data_list'
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149 - 'get_vpz_input' 'post_vpz_input'
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150 - 'get_vpz_output' 'post_vpz_output'
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151 - 'get_vpz_inout' 'post_vpz_inout'
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152 - 'get_vpz_experiment' 'post_vpz_experiment'
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153 - 'get_vpz_report_conditions' 'post_vpz_report_conditions'
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154 - 'get_vpz_report' 'post_vpz_report'
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155
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156 Code:
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157
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158 ----
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159
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160 - main_file.py
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161
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162 Inputs:
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163
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164 -------
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165
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166 - action value (mandatory)
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167
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168 - data json file (optional) (json file, param type="data")
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169 An action value that would be into data would be ignored
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170
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171 - experiment.xls (only in 'post_vpz_experiment' case)
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172
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173 - datafolder (optional) (only in cases :
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174 'post_vpz_experiment', 'post_vpz_report', 'post_vpz_output', 'post_vpz_inout')
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175
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176 Outputs:
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177
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178 --------
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179
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180 - data json file
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181
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182 - 1 other file (xls or zip) :
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183 - if 'action' == get_vpz_experiment, post_vpz_experiment :
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184 experiment.xls file
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185 - if 'action' == get_vpz_report_conditions, post_vpz_report_conditions :
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186 conditions.xls file
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187 - if 'action' == get_vpz_report, post_vpz_report :
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188 report.zip file
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189
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190 Credits:
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191
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192 --------
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193
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194 - Author: Nathalie Rousse nathalie.rousse@inrae.fr
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195 - Copyright: INRAE
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196
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197 ]]>
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198 </help>
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199
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200 </tool>
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201