# HG changeset patch
# User tduigou
# Date 1644318748 0
# Node ID 34a9d136a5bf42ed188c26f251e7f43d046ddd36
# Parent  481f7c35323d1b7a2ba6a2d0d7a7be9add4eee4c
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

diff -r 481f7c35323d -r 34a9d136a5bf selenzy.xml
--- 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>
\ No newline at end of file
diff -r 481f7c35323d -r 34a9d136a5bf test-data/uniprod_ids_out.xml
--- a/test-data/uniprod_ids_out.xml	Wed Dec 15 13:59:04 2021 +0000
+++ b/test-data/uniprod_ids_out.xml	Tue Feb 08 11:12:28 2022 +0000
@@ -23,51 +23,15 @@
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+      <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
+            <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
               <bqbiol:is>
                 <rdf:Bag/>
               </bqbiol:is>
             </rdf:Description>
-            <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/>
-                <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="MNXM83" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
-                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
-                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
-      <species metaid="_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb" id="MNXM35" name="MNXM35" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb">
+            <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
               <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
                 <brsynth:smiles/>
                 <brsynth:inchi/>
@@ -95,6 +59,24 @@
           </rdf:RDF>
         </annotation>
       </species>
+      <species metaid="_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb" id="MNXM35" name="MNXM35" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_53be86b11fa13c25dcb440bba6ef77b51b257a3674e6b2a0b88d272dc0a014cb">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles/>
+                <brsynth:inchi/>
+                <brsynth:inchikey/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
       <species metaid="_2c27bb432be6149f648dcec0e702fd9bdf6449fb9f730bd86eeb0b63b93d8858" id="CMPD_0000000003" name="CMPD_0000000003" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
@@ -149,19 +131,37 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39" id="MNXM24" name="MNXM24" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+      <species metaid="b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46" id="CMPD_0000000001" name="CMPD_0000000001" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
-            <rdf:Description rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
+            <rdf:Description rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
               <bqbiol:is>
                 <rdf:Bag/>
               </bqbiol:is>
             </rdf:Description>
-            <rdf:BRSynth rdf:about="#_61841f05183ff06dbe77a0e01f6d73d7a890997d823ac18d9fd56bac3d4bcc39">
+            <rdf:BRSynth rdf:about="#b0098569a07f786a6e9b2294639668cd4ee564dd642a38bdf429c4c6bb560b46">
               <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles/>
-                <brsynth:inchi/>
-                <brsynth:inchikey/>
+                <brsynth:smiles value="[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C40H64/c1-33(2)19-13-23-37(7)27-17-31-39(9)29-15-25-35(5)21-11-12-22-36(6)26-16-30-40(10)32-18-28-38(8)24-14-20-34(3)4/h11-12,19-22,27-30H,13-18,23-26,31-32H2,1-10H3"/>
+                <brsynth:inchikey value="YVLPJIGOMTXXLP-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0" id="MNXM83" name="MNXM83" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#_47d72a86d31940edf1cc42c7a7361a7a96211dc2a6679326b8ad27a7e216ada0">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])([H])C(=C([H])[H])C([H])([H])[H]"/>
+                <brsynth:inchi value="InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h1,3-4H2,2H3,(H,9,10)(H2,6,7,8)"/>
+                <brsynth:inchikey value="NUHSROFQTUXZQQ-UHFFFAOYSA-N"/>
               </brsynth:brsynth>
             </rdf:BRSynth>
           </rdf:RDF>
@@ -7888,8 +7888,8 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="CMPD_0000000003"/>
           <groups:member groups:idRef="CMPD_0000000001"/>
-          <groups:member groups:idRef="CMPD_0000000003"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_564fce39b23c6cf87d12dc2c612448384fd2cd980fe3fc07829e2ef802645579" groups:id="rp_trunk_species" groups:kind="collection">
@@ -7901,11 +7901,11 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
-          <groups:member groups:idRef="CMPD_0000000001"/>
-          <groups:member groups:idRef="MNXM83"/>
           <groups:member groups:idRef="MNXM34"/>
           <groups:member groups:idRef="CMPD_0000000003"/>
           <groups:member groups:idRef="TARGET_0000000001"/>
+          <groups:member groups:idRef="CMPD_0000000001"/>
+          <groups:member groups:idRef="MNXM83"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
@@ -7917,9 +7917,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
-          <groups:member groups:idRef="MNXM35"/>
+          <groups:member groups:idRef="MNXM24"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM24"/>
+          <groups:member groups:idRef="MNXM35"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
@@ -7931,9 +7931,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
-          <groups:member groups:idRef="MNXM83"/>
+          <groups:member groups:idRef="MNXM34"/>
           <groups:member groups:idRef="MNXM11"/>
-          <groups:member groups:idRef="MNXM34"/>
+          <groups:member groups:idRef="MNXM83"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="a0f48a6fe4f833a3d15abd7ee5b944b97d629570ac09588e9fb6fdf6196ab189" groups:id="rp_fba_ignored_species" groups:kind="collection">
@@ -7945,8 +7945,8 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
+          <groups:member groups:idRef="MNXM24"/>
           <groups:member groups:idRef="MNXM35"/>
-          <groups:member groups:idRef="MNXM24"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="fb9b29ba20af773fed953f1d6726905a453f235c9a4baa7217f02760bc2057f8" groups:id="rp_thermo_substituted_species" groups:kind="collection">
@@ -7958,9 +7958,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
-          <groups:member groups:idRef="MNXM35"/>
           <groups:member groups:idRef="MNXM24"/>
           <groups:member groups:idRef="TARGET_0000000001"/>
+          <groups:member groups:idRef="MNXM35"/>
         </groups:listOfMembers>
       </groups:group>
     </groups:listOfGroups>