diff sbml2sbol.xml @ 0:f0a06f526c7f draft

"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sbml2sbol.xml	Thu Dec 09 14:21:48 2021 +0000
@@ -0,0 +1,83 @@
+<tool id="sbml2sbol" name="SbmlToSbol" version="0.1.12">
+    <description>Convert sbml to sbol format</description>
+    <requirements>
+        <requirement type="package" version="0.1.12">sbml2sbol</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m sbml2sbol
+            --input '$sbml_single_input'
+            --outfile '$sbol_outfile'
+        #if str($adv.rbs) == "true"
+            --rbs True
+        #else
+            --rbs False
+        #end if
+        --max_prot_per_react '$adv.max_prot_per_react'
+        #if $adv.tirs 
+            --tirs $adv.tirs
+        #end if
+        --pathway_id '$adv.pathway_id'
+        --uniprotID_key '$adv.uniprotID_key'
+    ]]></command>
+    <inputs>
+        <param name="sbml_single_input" type="data" format="xml" label="Pathway (SBML)" />
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="rbs" type="boolean" label="Calculate the RBS strength?" checked="true" />
+            <param name="max_prot_per_react" type="integer" value="3" label="The maximum number of proteins per reaction" />
+            <param name="tirs" type="text" optional="true" label="Space separated RBS strength values" />
+            <param name="pathway_id" type="text" value="rp_pathway" label="Group ID of the heterologous pathway" />
+            <param name="uniprotID_key" type="text" value="selenzy" label="Uniprot ID" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="sbol_outfile" format="xml" label="${tool.name}: sbol outfile" />
+    </outputs>
+    <tests>
+        <test>
+        <!-- test 1: check if identical outputs are produced with default parameters  -->
+            <param name="sbml_single_input" value="lycopene.xml" />
+            <output name="sbol_outfile" file="sbol_lycopene_output.xml" ftype="xml" compare="diff" sort="true"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+SBML to SBOL
+================
+
+Convert a single or multiple SBML files to SBOL.
+
+Input
+-----
+
+Required:
+
+* **input**\ : (string) path to folder(s) containing rpSBML files and/or rpSBML file path(s).
+
+Advanced options:
+
+* **rbs**\ : (boolean) Calculate or not the RBS strength (default: True).
+* **max_prot_per_react**\ : (int) The maximum number of proteins per reaction (default: 3).
+* **tirs**\ : (int) The RBS strength values (default: None)
+* **pathway_id**\ : (string) Group ID of the heterologous pathway (default: rp_pathway)
+* **uniprotID_key**\ : (string) Group ID of the heterologous pathway (default: selenzy)
+
+Output
+------
+
+* **outfile**\ : (string) specify output (SBOL) file.
+
+Project Links
+------------------
+
+* `GitHub <https://github.com/neilswainston/SbmlToSbol>`_
+
+Version
+----------
+0.1.12
+
+License
+-------
+
+* `MIT <https://raw.githubusercontent.com/neilswainston/SbmlToSbol/master/LICENSE>`_
+
+    ]]></help>
+</tool>
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