--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rrparser/rrparser.xml	Wed Jul 07 09:18:49 2021 +0000
@@ -0,0 +1,119 @@
+<tool id="rrparser" name="RRules Parser" version="2.4.0">
+    <description>Reaction Rules Parser</description>
+    <requirements>
+        <requirement type="package">rrparser</requirement>
+    </requirements>
+    <stdio>
+        <regex match="WARNING:" level="warning" />
+	    <regex match="ERROR:" level="fatal" />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+        python -m rrparser
+        #if str($rules.type) != "other":
+            retrorules
+            --rule-type '$rules.type'
+        #else:
+            '$rules.file'
+            --input-format '$rules.format'
+        #end if
+        --diameters '$diameters'
+        --output-format csv
+        #if str($compress) == "true":
+            --outfile '$output'.csv.gz ;
+            mv '$output'.csv.gz '$output'
+        #else:
+            --outfile '$output'
+        #end if
+    ]]></command>
+    <inputs>
+        <conditional name="rules">
+            <param name="type" optional="True" type="select" label="Rule Type" help="">
+                <option value="retro" selected="True">RetroRules (retro)</option>
+                <option value="forward">RetroRules (forward)</option>
+                <option value="all">RetroRules (all)</option>
+                <option value="other">Other reaction rules...</option>
+            </param>
+            <when value="other">
+                <param name="file" optional="False" type="data" format="csv" label="Rules File"/>
+                <param name="format" optional="False" type="select" label="File format">
+                    <option value="csv" selected="True">csv</option>
+                    <option value="tsv">tsv</option>
+                </param>
+            </when>
+            <when value="retro|forward|all">
+                <param name="file" optional="True" type="data" format="csv" label="Rules File"/>
+            </when>
+        </conditional>
+        <param name="diameters" type="select" display="checkboxes" multiple="True" label="Select the diameters of the reactions rules">
+            <option selected="true" value="2">2</option>
+            <option selected="true" value="4">4</option>
+            <option selected="true" value="6">6</option>
+            <option selected="true" value="8">8</option>
+            <option selected="true" value="10">10</option>
+            <option selected="true" value="12">12</option>
+            <option selected="true" value="14">14</option>
+            <option selected="true" value="16">16</option>
+        </param>
+        <param name="compress" type="boolean" display="checkboxes" label="Compress output" />
+    </inputs>
+    <outputs>
+        <data name="output" format="csv" label="${tool.name} - ${rules.type} - d=$diameters" >
+            <change_format>
+                <when input="compress" value="true" format="csv.gz"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+        <!-- test 1: check if identical outputs are produced with compress option -->
+            <param name="compress" value="True" />
+            <output name="output" file="rules.csv.gz" compare="diff" decompress="True"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+RRulesParser
+============
+
+Retrieve the reaction rules from `RetroRules <https://retrorules.org/>`_
+
+Input
+-----
+
+* **rules-file**: (string) Filename of reaction rules
+* **input-format**: (string) Valid options: csv, tsv. Format of the input file
+* **rule-type**: (string) Valid options: retro, forward, all. Return the rules that are in reverse, forward or both direction
+* **diameters**: (integer list) Valid options: 2, 4, 6, 8, 10, 12, 14, 16. The diameter of the rules to return
+* **outdir**: (string) Path where output files will be written
+* **outfile**: (string) Path where output files will be written
+* **output-format**: (string) Valid options: csv, tar.gz. Format of the returned file
+
+Ouput
+-----
+
+* **output**: (string): Path of the output file. Either a compressed tar.gz (containing a csv) or csv list of reaction rules that are in a RetroPath2.0 friendly format
+
+
+Version
+-------
+
+v2.4.0
+
+Authors
+-------
+
+* **Thomas Duigou**
+* Melchior du Lac
+* Joan Hérisson
+
+License
+-------
+
+This project is licensed under the MIT License - see the `LICENSE <LICENSE>`_ file for details
+
+Acknowledgments
+---------------
+
+* Joan Hérisson
+
+    ]]></help>
+</tool>
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