diff selenzy.xml @ 1:34a9d136a5bf draft

"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

--- a/selenzy.xml	Wed Dec 15 13:59:04 2021 +0000
+++ b/selenzy.xml	Tue Feb 08 11:12:28 2022 +0000
@@ -1,27 +1,34 @@
-<tool id="selenzy-wrapper" name="Selenzyme" version="0.1.0">
+<tool id="selenzy-wrapper" name="Selenzyme" version="@TOOL_VERSION@" profile="19.09">
     <description>Performs enzyme selection from a reaction query</description>
-	<requirements>
-        <requirement type="package" version="0.1.0">selenzy_wrapper</requirement>
+    <macros>
+        <token name="@TOOL_VERSION@">0.2.0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">selenzy_wrapper</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-	    python -m selenzy_wrapper '$pathway' '$uniprot_ids'
+        python -m selenzy_wrapper '$pathway' '$uniprot_ids'
         --nb_targets '$adv.nb_targets'
         --d '$adv.direction'
         #if str($adv.NoMSA) == "false":
             --NoMSA
         #end if
-        --taxonIDs '$adv.taxonIDs'
+        --host_taxID '$adv.host_taxID'
+        #if str($adv.enzyme_taxIDs) != "":
+            --enzyme_taxIDs '$adv.enzyme_taxIDs'
+        #end if
         --nb_ids '$adv.nb_ids'
         --to_csv '$uniprot_ids_csv'
     ]]></command>
     <inputs>
-		<param name="pathway" type="data" format="xml" label="Pathway (SBML)" />
+        <param name="pathway" type="data" format="xml" label="Pathway (SBML)" />
         <section name="adv" title="Advanced Options" expanded="false">
-		    <param name="nb_ids"        type="integer" value="-1"       label="Number of uniprot IDs with top score to keep" />
-		    <param name="nb_targets"        type="integer" value="500"       label="Number of targets to display in results" />
-            <param name="direction"        type="float" value="0"       label="Use similiarity values for preferred reaction direction only" />
-            <param name="NoMSA"     type="boolean" label="Do not compute MSA/conservation scores ?"       checked="true"   display="checkboxes" />
-            <param name="taxonIDs" type="text" label="Comma separated taxon ids (first considered as the host)" value="83333" />
+            <param name="host_taxID" type="integer" value="83333" label="Host taxon ID" />
+            <param name="enzyme_taxIDs" type="text" value="" label="Comma separated taxon IDs of output enzyme sequences" />
+            <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" />
+            <param name="nb_targets" type="integer" value="500" label="Number of targets to display in results" />
+            <param name="direction" type="float" value="0" label="Use similiarity values for preferred reaction direction only" />
+            <param name="NoMSA" type="boolean" checked="true" display="checkboxes" label="Do not compute MSA/conservation scores ?" />
         </section>
     </inputs>
     <outputs>
@@ -50,7 +57,8 @@
 * **nb_ids**\ : (integer) Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]
 * **direction**\ : (float) Use similiarity values for preferred reaction direction only [default=0 (OFF)]
 * **NoMSA**\ : (boolean) Do not compute MSA/conservation scores
-* **taxonIDs**\ : (string) Comma separated taxon ids [default: 83333 (E. coli K12)]. The first taxon ID is the one of the chassis, following ones are taxon IDs of output enzyme sequences
+* **host_taxID**\ : (string) Taxon ID of the chassis (default: 83333 [E. coli K12])
+* **enzyme_taxIDs**\ : (string) Comma separated taxon IDs of output enzyme sequences
 
 Output
 ------
@@ -65,7 +73,7 @@
 Version
 ----------
 
-0.1.0
+0.2.0
 
 Authors
 -------
@@ -83,16 +91,6 @@
 
     ]]></help>
     <citations>
-        <citation type="bibtex">
-@article{10.1093/bioinformatics/bty065,
-  title={Selenzyme: enzyme selection tool for pathway design},
-  author={Pablo Carbonell, Jerry Wong, Neil Swainston, Eriko Takano, Nicholas J Turner, Nigel S Scrutton, Douglas B Kell, Rainer Breitling, Jean-Loup Faulon},
-  volume={34},
-  pages={2153–2154},
-  year={2018},
-  doi = {10.1093/bioinformatics/bty065},
-  url = {https://doi.org/10.1093/bioinformatics/bty065},
-}
-        </citation>
+        <citation type="doi">10.1093/bioinformatics/bty065</citation>
     </citations>
 </tool>
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