Mercurial > repos > siwaa > tabular_file_checker

annotate tfc.xml @ 0:9e72c0cef1f7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
author siwaa
date Mon, 10 Jul 2023 14:15:29 +0000
parents
children fb2d0a0a55eb
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
1 <tool id="tfc" name="TabularFileChecker" version="1.0.0">
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
2 <description>to check tabular files content and structure</description>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
3 <requirements>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
4 <container type="singularity">docker://registry.forgemia.inra.fr/record/tfc:latest</container>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
5 </requirements>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
6 <command detect_errors="aggressive">
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
7 <![CDATA[
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
8 cp ${tabularInput} ./input.csv &&
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
9 tfc genschema genschema ./input.csv &&
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
10 cp ./input*.json ${schema}
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
11 ]]>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
12 </command>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
13 <inputs>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
14 <param name="tabularInput" type="data" format="csv" label="Select a csv file to check"/>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
15 </inputs>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
16 <outputs>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
17 <data format="json" name="schema" label="${tabularInput.name} schema"/>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
18 </outputs>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
19 <tests>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
20 </tests>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
21 <help>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
22 Documentation
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
23 -------------
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
24 TODO
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
25
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
26 Credits
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
27 -------
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
28 - Galaxy Tool Maintainer: Patrick Chabrier patrick.chabrier@inrae.fr
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
29 - Copyright: INRAE
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
30 </help>
9e72c0cef1f7 "planemo upload for repository https://forgemia.inra.fr/record/tfc-/tree/main/tools/tfc commit 8ef27130c1fef3ba1e2dfa4a89d4d324b943a3b4"
siwaa
parents:
diff changeset
31 </tool>