diff get_sbml_model.xml @ 2:fa893f77dc22 draft

planemo upload for repository https://github.com/brsynth/synbiocad-galaxy-wrappers commit 18fcec17fb6415ad5a59b9bcfa853e755c768e6f

--- a/get_sbml_model.xml	Mon Apr 03 09:18:22 2023 +0000
+++ b/get_sbml_model.xml	Mon Apr 24 14:49:53 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="get_sbml_model" name="Pick SBML Model" version="0.0.2" profile="19.09" license="MIT">
+<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>
@@ -8,7 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
         curl -o - 'http://bigg.ucsd.edu/static/models/$(input).xml.gz'
         | gunzip > '$model';
-        python '$__tool_directory__/'get_infos.py '$model' --comp '$compartments' --biomass '$biomass'
+        python '$__tool_directory__/'get_infos.py '$model' --hostid '$input' --comp '$compartments' --biomass '$biomass' --taxid '$taxid'
     ]]></command>
     <inputs>
         <param name="input" type="select" label="Strain">
@@ -63,6 +63,7 @@
     </inputs>
     <outputs>
         <data name="model" format="sbml" label="${input}" />
+        <data name="taxid" format="tsv" label="${input} (taxon id)" />
         <data name="compartments" format="tsv" label="${input} (compartments)" />
         <data name="biomass" format="tsv" label="${input} (biomass reactions)" />
     </outputs>
@@ -71,7 +72,8 @@
         <!-- test 1: check if identical outputs are produced with iML1515 model input  -->
             <param name="input" value="iML1515" />
             <output name="model" md5="9bf81d20cab5476700697ded95b716d1"/>
-            <output name="comp" md5="e93a875a2d8efc10a880ae3ac0018236"/>
+            <output name="taxid" md5="ec29688652dd49becf7be2a6c2469287"/>
+            <output name="compartments" md5="e93a875a2d8efc10a880ae3ac0018236"/>
             <output name="biomass" md5="cffb2fbdb07d1301dfdb7bb284fb7e06"/>
         </test>
     </tests>
@@ -84,4 +86,13 @@
     <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+            @unpublished{get_sbml_model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>