# HG changeset patch
# User tduigou
# Date 1644247449 0
# Node ID 8e56fc458ca5d4ba24e3ee2c178ed7f1cd7ab2e5
# Parent  8a04f97b785dc3f30447864ccae29b8866b837d3
"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

diff -r 8a04f97b785d -r 8e56fc458ca5 retropath2.xml
--- a/retropath2.xml	Mon Feb 07 15:20:35 2022 +0000
+++ b/retropath2.xml	Mon Feb 07 15:24:09 2022 +0000
@@ -1,14 +1,17 @@
-<tool id="retropath2" name="RetroPath2.0" version="2.3.0">
+<tool id="retropath2" name="RetroPath2.0" version="@TOOL_VERSION@" profile="19.09">
     <description>Build a reaction network from a set of source compounds to a set of sink compounds</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.3.0</token>
+    </macros>
     <requirements>
-        <requirement type="package" version="2.3.0">retropath2_wrapper</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">retropath2_wrapper</requirement>
     </requirements>
     <stdio>
-        <exit_code range="1" level="fatal"   description="Source has been found in the sink"                          />
-        <exit_code range="2" level="fatal"   description="Cannot find source-in-sink file"                            />
-        <exit_code range="3" level="fatal"   description="Running the RetroPath2.0 Knime program produced an OSError" />
-        <exit_code range="4" level="warning" description="RetroPath2.0 has found no solution"                         />
-        <exit_code range="5" level="warning" description="Time limit reached"                                         />
+        <exit_code range="1" level="fatal" description="Source has been found in the sink" />
+        <exit_code range="2" level="fatal" description="Cannot find source-in-sink file" />
+        <exit_code range="3" level="fatal" description="Running the RetroPath2.0 Knime program produced an OSError" />
+        <exit_code range="4" level="warning" description="RetroPath2.0 has found no solution" />
+        <exit_code range="5" level="warning" description="Time limit reached" />
 	</stdio>
     <command detect_errors="exit_code"><![CDATA[
         python -m retropath2_wrapper
@@ -18,22 +21,21 @@
             --source_inchi '$source_inchi_type.source_inchi'
             --source_name '$source_name'
             --rp2_version '$adv.version'
-            --max_steps '$adv.max_steps'
+            --max_steps '$max_steps'
             --topx '$adv.topx'
             --dmin '$adv.dmin'
             --dmax '$adv.dmax'
             --mwmax_source '$adv.mwmax_source'
-            --mwmax_cof '$adv.mwmax_cof'
-            --timeout '$adv.timeout';
+            --timeout '$adv.timeout' &&
         if compgen -G 'out/*_scope.csv' > /dev/null; then
-            cp out/*_scope.csv '$Reaction_Network';
+            cp 'out/*_scope.csv' '$Reaction_Network';
         else
-            cp out/results.csv '$Reaction_Network';
+            cp 'out/results.csv' '$Reaction_Network';
         fi
     ]]></command>
     <inputs>
-        <param name="rulesfile"    type="data" format="csv" label="Rules File"/>
-        <param name="sinkfile"     type="data" format="csv" label="Sink File"/>
+        <param name="rulesfile" type="data" format="csv,tar" label="Rules File"/>
+        <param name="sinkfile" type="data" format="csv" label="Sink File"/>
         <conditional name="source_inchi_type">
             <param name="inchi_type" type="select" label="InChI type">
                 <!-- <option value="name" selected="true">By name</option> -->
@@ -45,20 +47,21 @@
                 </param>
             </when>
         </conditional>
-        <param name="source_name" type="text" value="target" optional="true" label="Source name"/>
+        <param name="max_steps" type="integer" value="3" min="1" max="10" label="Maximal Pathway length" />
+        <param name="source_name" type="text" value="target" optional="true" label="Source name">
+            <validator type="empty_field" message="Source name is required"/>
+        </param>
         <section name="adv" title="Advanced Options" expanded="false">
             <param name="version" type="select" label="Workflow version">
                 <option value="v9">v9</option>
                 <option value="r20210127">r20210127</option>
                 <option value="r20220104" selected="true">r20220104</option>
             </param>
-            <param name="max_steps"    type="integer" value="3"    label="Maximal Pathway length" />
-            <param name="topx"         type="integer" value="100"  label="TopX"                                  />
-            <param name="dmin"         type="integer" value="0"    label="Minimum rule diameter"                 />
-            <param name="dmax"         type="integer" value="1000" label="Maximum rule diameter"                 />
-            <param name="mwmax_source" type="integer" value="1000" label="Molecular weight of source (Da)"       />
-            <param name="mwmax_cof"    type="integer" value="1000" label="Molecular weight of cofactors (Da)" />
-            <param name="timeout"      type="integer" value="60"   label="Timeout (min)"                         />
+            <param name="topx" type="integer" value="100" min="1" max="1000" label="TopX" />
+            <param name="dmin" type="integer" value="0" min="0" max="1000" label="Minimum rule diameter" />
+            <param name="dmax" type="integer" value="1000" min="0" max="1000" label="Maximum rule diameter" />
+            <param name="mwmax_source" type="integer" value="1000" min="0" max="2000" label="Molecular weight of source (Da)" />
+            <param name="timeout" type="integer" value="60" min="30" max="600" label="Timeout (min)" />
         </section>
     </inputs>
     <outputs>
@@ -103,7 +106,6 @@
 * **-dmin**\ : (integer, default: 0)
 * **-dmax**\ : (integer, default: 1000)
 * **-mwmax_source**\ : (integer, default: 1000)
-* **-mwmax_cof**\ : (integer, default: 1000)
 * **-timeout**\ : (integer, default: 30) Timeout in minutes
 
 Output
@@ -129,15 +131,6 @@
 
     ]]></help>
     <citations>
-        <citation type="bibtex">
-@article{delepine2018retropath2,
-  title={RetroPath2. 0: a retrosynthesis workflow for metabolic engineers},
-  author={Del{\'e}pine, Baudoin and Duigou, Thomas and Carbonell, Pablo and Faulon, Jean-Loup},
-  journal={Metabolic engineering},
-  volume={45},
-  pages={158--170},
-  year={2018},
-  publisher={Elsevier}}
-        </citation>
+        <citation type="doi">10.1016/j.ymben.2017.12.002 </citation>
     </citations>
 </tool>
\ No newline at end of file
diff -r 8a04f97b785d -r 8e56fc458ca5 test-data/results_retropath2.csv
--- a/test-data/results_retropath2.csv	Mon Feb 07 15:20:35 2022 +0000
+++ b/test-data/results_retropath2.csv	Mon Feb 07 15:24:09 2022 +0000
@@ -1,43 +1,9 @@
 "Initial source","Transformation ID","Reaction SMILES","Substrate SMILES","Substrate InChI","Product SMILES","Product InChI","In Sink","Sink name","Diameter","Rule ID","EC number","Score","Starting Source SMILES","Iteration"
-"[target]","TRS_0_0_0","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]>>O=O.[H]Oc1c([H])c([H])c([H])c([H])c1O[H]","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","InChI=1S/C6H6O4/c7-5(8)3-1-2-4-6(9)10/h1-4H,(H,7,8)(H,9,10)","O=O","InChI=1S/O2/c1-2","1","[MNXM4]","16","[RR-02-a0cc0be463ff412f-16-F]","[1.13.11.1]","0.9542425094393248","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","0"
-"[target]","TRS_0_0_0","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]>>O=O.[H]Oc1c([H])c([H])c([H])c([H])c1O[H]","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","InChI=1S/C6H6O4/c7-5(8)3-1-2-4-6(9)10/h1-4H,(H,7,8)(H,9,10)","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]","InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H","0","[None]","16","[RR-02-a0cc0be463ff412f-16-F]","[1.13.11.1]","0.9542425094393248","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","0"
-"[target]","TRS_0_1_0","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]>>O=O.[H+].[H]c1c([H])c([H])c(N([H])[H])c([H])c1[H]","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]","InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H","[H+]","InChI=1S","1","[MNXM1]","16","[RR-02-08eb71f5bf7680a5-16-F]","[1.14.-.-]","1.3802112417116061","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","1"
-"[target]","TRS_0_1_0","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]>>O=O.[H+].[H]c1c([H])c([H])c(N([H])[H])c([H])c1[H]","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]","InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H","O=O","InChI=1S/O2/c1-2","1","[MNXM4]","16","[RR-02-08eb71f5bf7680a5-16-F]","[1.14.-.-]","1.3802112417116061","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","1"
-"[target]","TRS_0_1_10","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]>>O=O.[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H].[H]OC(=O)c1c([H])c([H])c([H])c([H])c1O[H]","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]","InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H","O=O","InChI=1S/O2/c1-2","1","[MNXM4]","16","[RR-02-36106ef8d9461f98-16-F]","[1.14.13.1]","0.3010299956639812","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","1"
-"[target]","TRS_0_1_10","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]>>O=O.[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H].[H]OC(=O)c1c([H])c([H])c([H])c([H])c1O[H]","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]","InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H","[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H]","InChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)","1","[MNXM10]","16","[RR-02-36106ef8d9461f98-16-F]","[1.14.13.1]","0.3010299956639812","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","1"
-"[target]","TRS_0_1_13","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]>>O=O.[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H].[H]Oc1c([H])c([H])c([H])c([H])c1[H]","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]","InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H","O=O","InChI=1S/O2/c1-2","1","[MNXM4]","16","[RR-02-0a885fdec2a1ff5f-16-F]","[1.14.13.-, 1.14.13.M20]","1.0791812460476249","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","1"
-"[target]","TRS_0_1_13","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]>>O=O.[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H].[H]Oc1c([H])c([H])c([H])c([H])c1[H]","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]","InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H","[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H]","InChI=1S/C21H29N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1,3-4,7-8,10-11,13-16,20-21,29-32H,2,5-6H2,(H2,23,33)(H,34,35)(H,36,37)(H2,22,24,25)","1","[MNXM10]","16","[RR-02-0a885fdec2a1ff5f-16-F]","[1.14.13.-, 1.14.13.M20]","1.0791812460476249","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","1"
-"[target]","TRS_0_1_16","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]>>O=O.[H]Oc1c([H])c([H])c([H])c([H])c1[H]","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]","InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H","O=O","InChI=1S/O2/c1-2","1","[MNXM4]","16","[RR-02-f499af41ee160034-16-F]","[1.14.18.1]","1.6127838567197357","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","1"
-"[target]","TRS_0_1_2","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]>>O=O.[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H].[H]OC(=O)c1c([H])c([H])c([H])c([H])c1N([H])[H]","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]","InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H","O=O","InChI=1S/O2/c1-2","1","[MNXM4]","16","[RR-02-9137e79005134eeb-16-F]","[1.14.12.1]","0.7781512503836436","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","1"
-"[target]","TRS_0_1_2","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]>>O=O.[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H].[H]OC(=O)c1c([H])c([H])c([H])c([H])c1N([H])[H]","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]","InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H","[H]OC(=O)c1c([H])c([H])c([H])c([H])c1N([H])[H]","InChI=1S/C7H7NO2/c8-6-4-2-1-3-5(6)7(9)10/h1-4H,8H2,(H,9,10)","1","[MNXM188]","16","[RR-02-9137e79005134eeb-16-F]","[1.14.12.1]","0.7781512503836436","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","1"
-"[target]","TRS_0_1_2","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]>>O=O.[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H].[H]OC(=O)c1c([H])c([H])c([H])c([H])c1N([H])[H]","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]","InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H","[H]N=C(O[H])C1=C([H])N(C2([H])OC([H])(C([H])([H])OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C3([H])OC([H])(n4c([H])nc5c(N([H])[H])nc([H])nc54)C([H])(OP(=O)(O[H])O[H])C3([H])O[H])C([H])(O[H])C2([H])O[H])C([H])=C([H])C1([H])[H]","InChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)","1","[MNXM6]","16","[RR-02-9137e79005134eeb-16-F]","[1.14.12.1]","0.7781512503836436","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","1"
-"[target]","TRS_0_1_20","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]>>[H]OC(=O)c1c([H])c([H])c([H])c(O[H])c1O[H]","[H]Oc1c([H])c([H])c([H])c([H])c1O[H]","InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H","[H]OC(=O)c1c([H])c([H])c([H])c(O[H])c1O[H]","InChI=1S/C7H6O4/c8-5-3-1-2-4(6(5)9)7(10)11/h1-3,8-9H,(H,10,11)","1","[MNXM455]","16","[RR-02-876f09a1ab1b55e5-16-F]","[4.1.1.46]","0.3010299956639812","[H]OC(=O)C([H])=C([H])C([H])=C([H])C(=O)O[H]","1"
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