diff get_sbml_model.xml @ 1:e276119e73c8 draft

planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3

--- a/get_sbml_model.xml	Tue Jan 11 16:15:04 2022 +0000
+++ b/get_sbml_model.xml	Mon Apr 24 13:26:25 2023 +0000
@@ -1,12 +1,14 @@
-<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.1" profile="19.09">
-    <description>Pick an SBML model among a list</description>
+<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.3" profile="19.09" license="MIT">
+    <description>Get an SBML model (BiGG)</description>
     <requirements>
         <requirement type="package" version="7.81.0">curl</requirement>
         <requirement type="package" version="1.11">gzip</requirement>
+        <requirement type="package" version="5.19.2">python-libsbml</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz'
-        | gunzip > '$sbml_model'
+        | gunzip > '$model';
+        python '$__tool_directory__/'get_infos.py '$model' --comp '$compartments' --biomass '$biomass'
     ]]></command>
     <inputs>
         <param name="input" type="select" label="Strain">
@@ -60,13 +62,17 @@
         </param>
     </inputs>
     <outputs>
-        <data name="sbml_model" format="xml" label="${tool.name} - ${input}" />
+        <data name="model" format="sbml" label="${input}" />
+        <data name="compartments" format="tsv" label="${input} (compartments)" />
+        <data name="biomass" format="tsv" label="${input} (biomass reactions)" />
     </outputs>
     <tests>
         <test>
         <!-- test 1: check if identical outputs are produced with iML1515 model input  -->
             <param name="input" value="iML1515" />
-            <output name="sbml_model" md5="9bf81d20cab5476700697ded95b716d1"/>
+            <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/>
+            <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236"/>
+            <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -74,29 +80,17 @@
 =================
 
 Download the selected SBML model fromg BiGG database.
-
-
-Version
-----------
-0.0.1
-
-
-Authors
--------
-
-* Joan Hérisson
-
-
-License
--------
-
-`MIT <https://github.com/brsynth/rptools/blob/master/LICENSE>`_
-
-
-Acknowledgments
----------------
-
-* Kenza Bazi-Kabbaj
-
     ]]></help>
-</tool>
\ No newline at end of file
+    <creator>
+        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
+    </creator>
+    <citations>
+        <citation type="bibtex">
+            @unpublished{get_sbml_model
+                author = {Joan Hérisson},
+                title = {{get_sbml_model}},
+                url = {https://github.com/brsynth/},
+            }
+        </citation>
+    </citations>
+</tool>