Mercurial > repos > tduigou > rrparser

changeset 13:a76972fe49bc draft default tip

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planemo upload for repository https://github.com/brsynth/rrparser commit 15dbdd1f0a222a8e1b0fb5c16b36885520a3d005
author tduigou
date Mon, 07 Apr 2025 07:47:30 +0000
parents 17fbb6aa450b
children
files rrparser.xml test-data/ec.csv test-data/ec.txt
diffstat 3 files changed, 7 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/rrparser.xml	Wed Apr 02 13:40:57 2025 +0000
+++ b/rrparser.xml	Mon Apr 07 07:47:30 2025 +0000
@@ -1,7 +1,7 @@
 <tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2" license="MIT">
     <description>Retrieve the reaction rules from RetroRules</description>
     <macros>
-        <token name="@VERSION_SUFFIX@">3</token>
+        <token name="@VERSION_SUFFIX@">4</token>
         <token name="@TOOL_VERSION@">2.7.0</token>
     </macros>
     <requirements>
@@ -69,10 +69,10 @@
                 </param>
                 <when value="no" />
                 <when value="in">
-                    <param name="input_ec_in" type="data" format="csv" label="File containing EC numbers" help="EC numbers on one line separted by a comma" />
+                    <param name="input_ec_in" type="data" format="txt" label="File containing EC numbers" help="EC numbers on one line separted by a comma" />
                 </when>
                 <when value="out">
-                    <param name="input_ec_out" type="data" format="csv" label="File containing EC numbers" help="EC numbers on one line separted by a comma" />
+                    <param name="input_ec_out" type="data" format="txt" label="File containing EC numbers" help="EC numbers on one line separted by a comma" />
                 </when>
             </conditional>
             <param argument="--diameters" type="select" display="checkboxes" multiple="True" label="Select the diameters of the reactions rules" help=" Diameter of the sphere including the atoms around the reacting center (default is including all values: 2,4,6,8,10,12,14,16). The higher is the diameter, the more specific are the rules">
@@ -124,13 +124,13 @@
             <section name="adv">
                 <conditional name="input_conditional_ec">
                     <param name="input_type" value="in"/>
-                    <param name="input_ec_in" value="ec.csv"/>
+                    <param name="input_ec_in" value="ec.txt"/>
                 </conditional>
             </section>
             <output name="out_rules" file="test.4.output.csv" ftype="csv" compare="diff"/>
         </test>
         <test>
-            <!-- python -m rrparser -rules_file rules_in.csv -input-format csv -ecx ec.csv -diameters 2,4,6,8,10,12,14,16 -output-format csv -outfile test.5.output.csv -->
+            <!-- python -m rrparser -rules_file rules_in.csv -input-format csv -ecx ec.txt -diameters 2,4,6,8,10,12,14,16 -output-format csv -outfile test.5.output.csv -->
             <conditional name="rules">
                 <param name="type" value="rules-file"/>
                 <param name="file" value="rules_in.csv" />
@@ -138,7 +138,7 @@
             <section name="adv">
                 <conditional name="input_conditional_ec">
                     <param name="input_type" value="out"/>
-                    <param name="input_ec_out" value="ec.csv"/>
+                    <param name="input_ec_out" value="ec.txt"/>
                 </conditional>
             </section>
             <output name="out_rules" file="test.5.output.csv" ftype="csv" compare="diff"/>
--- a/test-data/ec.csv	Wed Apr 02 13:40:57 2025 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-1.1.1.202,2.3.1.40,NOEC,1.2.3,2.4.1
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ec.txt	Mon Apr 07 07:47:30 2025 +0000
@@ -0,0 +1,1 @@
+1.1.1.202,2.3.1.40,NOEC,1.2.3,2.4.1
\ No newline at end of file