diff rrparser.xml @ 5:d7882cf07d98 draft

planemo upload for repository https://github.com/brsynth/rrparser commit eadd9bb9edbc70361b9e8d7900e6743b37142ee3

--- a/rrparser.xml	Tue Jun 21 14:39:03 2022 +0000
+++ b/rrparser.xml	Mon Apr 24 13:32:41 2023 +0000
@@ -1,8 +1,8 @@
-<tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
+<tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09" license="MIT">
     <description>Retrieve the reaction rules from RetroRules</description>
     <macros>
         <token name="@VERSION_SUFFIX@">0</token>
-        <token name="@TOOL_VERSION@">2.4.6</token>
+        <token name="@TOOL_VERSION@">2.5.2</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
@@ -14,14 +14,15 @@
     <command detect_errors="exit_code"><![CDATA[
         python -m rrparser
         #if str($rules.type) != "rules-file":
-            retrorules
+            --rules_file retrorules
             --rule-type '$rules.type'
         #else:
-            '$rules.file'
+            --rules_file '$rules.file'
             --input-format '$rules.input_format'
         #end if
         --diameters '$diameters'
         --output-format csv
+        --rules-dir "\${TMPDIR:-.}"
         #if str($compress) == "true":
             --outfile '$out_rules'.csv.gz
             && mv '$out_rules'.csv.gz '$out_rules'
@@ -37,6 +38,9 @@
                 <option value="all">RetroRules (all)</option>
                 <option value="rules-file">Other reaction rules...</option>
             </param>
+            <when value="retro"/>
+            <when value="forward"/>
+            <when value="all"/>
             <when value="rules-file">
                 <param name="file" type="data" format="csv" optional="False" label="Rules File" help="Filename of reaction rules"/>
                 <param name="input_format" type="select" optional="False" label="File format" help="Input file format (default: csv)">
@@ -103,31 +107,11 @@
 -----
 
 * **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes.
-
-Version
--------
-
-v2.4.6
-
-Authors
--------
-
-* **Thomas Duigou**
-* Melchior du Lac
-* Joan Hérisson
-
-License
--------
-
-This project is licensed under the MIT License - see the `LICENSE <https://github.com/brsynth/RRParser/blob/master/LICENSE>`_ file for details
-
-Acknowledgments
----------------
-
-* Joan Hérisson
-
     ]]></help>
+    <creator>
+        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
+    </creator>
     <citations>
-        <citation type="doi">10.1093/nar/gky940 </citation>
+        <citation type="doi">10.1093/nar/gky940</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>