Mercurial > repos > tduigou > rptools_rpextractsink

changeset 3:d9287c69a7f4 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rptools commit 044274b46d50a1d0e3708e80e0dfecf1de653c65
author tduigou
date Thu, 02 Nov 2023 14:37:08 +0000
parents caf2b5731a5e
children a21285560b16
files macros.xml rpextractsink.xml test-data/scored_pathway.xml
diffstat 3 files changed, 43 insertions(+), 49 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Mar 28 12:11:14 2023 +0000
+++ b/macros.xml	Thu Nov 02 14:37:08 2023 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">6.2.3</token>
+    <token name="@TOOL_VERSION@">6.3.2</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
--- a/rpextractsink.xml	Tue Mar 28 12:11:14 2023 +0000
+++ b/rpextractsink.xml	Thu Nov 02 14:37:08 2023 +0000
@@ -11,8 +11,9 @@
         python -m rptools.rpextractsink
             '$input'
             '$sink'
-            --compartment_id '$compartment_id'
+            --compartment-id '$compartment_id'
             $adv.remove_dead_end
+            $adv.standalone
             --cache-dir "\${TMPDIR:-.}"
     ]]></command>
     <inputs>
@@ -21,7 +22,8 @@
             <validator type="empty_field" message="SBML compartment ID is required"/>
         </param>
         <section name="adv" title="Advanced Options" expanded="false">
-            <param argument="--remove_dead_end" type="boolean" truevalue="--remove_dead_end" falsevalue="" checked="true" label="Remove dead-end metabolites using FVA evaluation?" help="Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites" />
+            <param argument="--remove_dead_end" type="boolean" truevalue="--remove-dead-end" falsevalue="" checked="true" label="Remove dead-end metabolites using FVA evaluation?" help="Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites" />
+            <param argument="--standalone" type="boolean" truevalue="--standalone" falsevalue="" checked="true" label="Do not connect to Internet" help="If True, do not retrieve InChI from Internet" />
         </section>
     </inputs>
     <outputs>
@@ -31,7 +33,7 @@
         <test>
         <!-- test 1: check if identical outputs are produced with iCN718 model input  -->
             <param name="input" value="iCN718.xml.gz" />
-            <output name="sink" md5="0a7438b90704bf1ba88e123e6bb54df2" />
+            <output name="sink" md5="5ff3987609142e828ec8e3c97b8dab12" />
         </test>
     </tests>
     <help><![CDATA[
@@ -55,6 +57,7 @@
 Advanced options:
 
 * **Remove dead-end metabolites using FVA evaluation?**\ : (boolean, default: True) Perform FVA (Flux Variability Analysis) evaluation to remove dead end metabolites.
+* **Do not connect to Internet**: (boolean, default: False) If True, do not retrieve InChI from Internet
 
 Output
 ------
--- a/test-data/scored_pathway.xml	Tue Mar 28 12:11:14 2023 +0000
+++ b/test-data/scored_pathway.xml	Thu Nov 02 14:37:08 2023 +0000
@@ -8,13 +8,9 @@
             <rdf:Description rdf:about="#_2e7d2c03a9507ae265ecf5b5356885a53393a2029d241394997265a1a25aefc6">
               <bqbiol:is>
                 <rdf:Bag>
-                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c"/>
-                  <rdf:li rdf:resource="http://identifiers.org/bigg.compartment/c_c"/>
-                  <rdf:li rdf:resource="http://identifiers.org/metanetx.compartment/MNXC3"/>
                   <rdf:li rdf:resource="http://identifiers.org/seed/c"/>
                   <rdf:li rdf:resource="http://identifiers.org/seed/c0"/>
                   <rdf:li rdf:resource="http://identifiers.org/seed/cytosol"/>
-                  <rdf:li rdf:resource="http://identifiers.org/name/cytosol"/>
                 </rdf:Bag>
               </bqbiol:is>
             </rdf:Description>
@@ -23,19 +19,19 @@
       </compartment>
     </listOfCompartments>
     <listOfSpecies>
-      <species metaid="fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9" id="MNXM97" name="MNXM97" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+      <species metaid="_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251" id="MNXM13" name="MNXM13" 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="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
+            <rdf:Description rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
               <bqbiol:is>
                 <rdf:Bag/>
               </bqbiol:is>
             </rdf:Description>
-            <rdf:BRSynth rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
+            <rdf:BRSynth rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
               <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
-                <brsynth:inchi value="InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)"/>
-                <brsynth:inchikey value="COLNVLDHVKWLRT-UHFFFAOYSA-N"/>
+                <brsynth:smiles value="O=C=O"/>
+                <brsynth:inchi value="InChI=1S/CO2/c2-1-3"/>
+                <brsynth:inchikey value="CURLTUGMZLYLDI-UHFFFAOYSA-N"/>
               </brsynth:brsynth>
             </rdf:BRSynth>
           </rdf:RDF>
@@ -59,19 +55,37 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251" id="MNXM13" name="MNXM13" compartment="c" initialConcentration="1" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false">
+      <species metaid="_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b" id="MNXM15" name="MNXM15" 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="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
+            <rdf:Description rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
               <bqbiol:is>
                 <rdf:Bag/>
               </bqbiol:is>
             </rdf:Description>
-            <rdf:BRSynth rdf:about="#_2a301e4e848a79652a3993832c9d968953ade64ccc71ea0ef1c47184f60ec251">
+            <rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
               <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="O=C=O"/>
-                <brsynth:inchi value="InChI=1S/CO2/c2-1-3"/>
-                <brsynth:inchikey value="CURLTUGMZLYLDI-UHFFFAOYSA-N"/>
+                <brsynth:smiles value="N"/>
+                <brsynth:inchi value="InChI=1S/H3N/h1H3"/>
+                <brsynth:inchikey value="QGZKDVFQNNGYKY-UHFFFAOYSA-N"/>
+              </brsynth:brsynth>
+            </rdf:BRSynth>
+          </rdf:RDF>
+        </annotation>
+      </species>
+      <species metaid="fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9" id="MNXM97" name="MNXM97" 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="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
+              <bqbiol:is>
+                <rdf:Bag/>
+              </bqbiol:is>
+            </rdf:Description>
+            <rdf:BRSynth rdf:about="#fc3a2e5cd1a81a37f4065ad4b53b9e5009ace624c22100af7e69653ca4a2eae9">
+              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
+                <brsynth:smiles value="[H]OC(=O)C([H])(N([H])[H])C([H])([H])c1c([H])c([H])c([H])c([H])c1[H]"/>
+                <brsynth:inchi value="InChI=1S/C9H11NO2/c10-8(9(11)12)6-7-4-2-1-3-5-7/h1-5,8H,6,10H2,(H,11,12)"/>
+                <brsynth:inchikey value="COLNVLDHVKWLRT-UHFFFAOYSA-N"/>
               </brsynth:brsynth>
             </rdf:BRSynth>
           </rdf:RDF>
@@ -113,24 +127,6 @@
           </rdf:RDF>
         </annotation>
       </species>
-      <species metaid="_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b" id="MNXM15" name="MNXM15" 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="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
-              <bqbiol:is>
-                <rdf:Bag/>
-              </bqbiol:is>
-            </rdf:Description>
-            <rdf:BRSynth rdf:about="#_70815415d0cc5bdb32d594ff385cc7e2e02e73da1f5099a321b65aa158a4cf7b">
-              <brsynth:brsynth xmlns:brsynth="http://brsynth.eu">
-                <brsynth:smiles value="N"/>
-                <brsynth:inchi value="InChI=1S/H3N/h1H3"/>
-                <brsynth:inchikey value="QGZKDVFQNNGYKY-UHFFFAOYSA-N"/>
-              </brsynth:brsynth>
-            </rdf:BRSynth>
-          </rdf:RDF>
-        </annotation>
-      </species>
     </listOfSpecies>
     <listOfParameters>
       <parameter metaid="dc937b59892604f5a86ac96936cd7ff09e25f18ae6b758e8014a24c7fa039e91" sboTerm="SBO:0000625" id="BRS_FBC_10000_0" value="10000" constant="true"/>
@@ -142,10 +138,7 @@
           <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="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
               <bqbiol:is>
-                <rdf:Bag>
-                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.24"/>
-                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.3.1.25"/>
-                </rdf:Bag>
+                <rdf:Bag/>
               </bqbiol:is>
             </rdf:Description>
             <rdf:BRSynth rdf:about="#_7af1776cbbaecbf874d7f576d21891f6ad79e3b7c2e726cfd2ee9f5bd6f483c4">
@@ -204,9 +197,7 @@
           <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="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
               <bqbiol:is>
-                <rdf:Bag>
-                  <rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.1.102"/>
-                </rdf:Bag>
+                <rdf:Bag/>
               </bqbiol:is>
             </rdf:Description>
             <rdf:BRSynth rdf:about="#c9c2d56fd0ad9d5b8cd80acad4b5df22945ab4de50db7b24db52a91a7560c3ff">
@@ -326,9 +317,9 @@
           </rdf:RDF>
         </annotation>
         <groups:listOfMembers>
-          <groups:member groups:idRef="TARGET_0000000001"/>
+          <groups:member groups:idRef="CMPD_0000000002"/>
           <groups:member groups:idRef="MNXM97"/>
-          <groups:member groups:idRef="CMPD_0000000002"/>
+          <groups:member groups:idRef="TARGET_0000000001"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_9e3154173c97366b3980dd1642e1e35d0bdfc3274abc744e89ecb518bcd48378" groups:id="rp_completed_species" groups:kind="collection">
@@ -341,8 +332,8 @@
         </annotation>
         <groups:listOfMembers>
           <groups:member groups:idRef="MNXM13"/>
+          <groups:member groups:idRef="MNXM15"/>
           <groups:member groups:idRef="MNXM1"/>
-          <groups:member groups:idRef="MNXM15"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="_58b3b59284e0d918d6d3f3bcadc2d757726da7594cd899cad4e745836ac967a3" groups:id="rp_sink_species" groups:kind="collection">
@@ -355,8 +346,8 @@
         </annotation>
         <groups:listOfMembers>
           <groups:member groups:idRef="MNXM13"/>
+          <groups:member groups:idRef="MNXM15"/>
           <groups:member groups:idRef="MNXM1"/>
-          <groups:member groups:idRef="MNXM15"/>
           <groups:member groups:idRef="MNXM97"/>
         </groups:listOfMembers>
       </groups:group>