diff rp2paths.xml @ 0:1e7007e80a4b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rp2paths commit c7d83bf1145bcd43d933d91d5a39af58b8f1834c

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+++ b/rp2paths.xml	Mon Oct 17 21:20:40 2022 +0000
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+<tool id="rp2paths" name="RP2paths" version="@TOOL_VERSION@" profile="21.09">
+    <description>Enumerate and seperate the different pathways generated by RetroPath2.0</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.5.0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">rp2paths</requirement>
+    </requirements>
+    <stdio>
+        <regex match="TIMEOUT:" level="fatal" />
+        <regex match="ERROR:"   level="fatal" />
+        <regex match="WARNING:" level="warning" />
+    </stdio>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir out &&
+        python -m rp2paths all
+        '$rp2_pathways'
+        --outdir out
+        --timeout '$adv.timeout' &&
+        cp out/compounds.txt '$compounds' &&
+        if test -f 'out/out_paths.csv'; then
+            cp out/out_paths.csv '$master_pathways';
+        fi
+    ]]></command>
+    <inputs>
+        <param name="rp2_pathways" type="data" format="csv" label="RetroPath2.0 Pathways" help="Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis."/>
+        <section name="adv" title="Advanced Options" expanded="false">
+            <param name="timeout" type="integer" value="1800" label="Time Out" help="Time out before killing a process (in seconds), default: 30 minutes." />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="master_pathways" format="csv" label="${tool.name} on ${rp2_pathways.name} : Enumerated Pathways" />
+        <data name="compounds" format="tabular" label="${tool.name} on ${rp2_pathways.name} : Compounds" />
+    </outputs>
+    <tests>
+        <test>
+            <!-- test 1: check if identical outputs are produced with default parameters  -->
+            <param name="rp2_pathways" value="retropath2_pathways.csv" />
+            <output name="master_pathways" file="rp2paths_pathways.csv" ftype="csv" compare="diff"/>
+            <output name="compounds" file="rp2paths_compounds.tsv" ftype="tabular" compare="diff"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+RP2paths
+========
+
+
+**RP2paths** extracts the set of heterologous pathways that lies in a metabolic space file outputted by the `RetroPath2.0 workflow <https://www.myexperiment.org/workflows/4987.html>`_ into individual pathways and enumerate them. This analysis is required to ensure that only pathways fulfilling all the precursor needs are retained for further analysis. This tool takes as input a retrosynthesis network in the CSV file produced by `RetroPath2.0 <https://toolshed.g2.bx.psu.edu/view/tduigou/retropath2/9c8ac9980bd6>`_ , and outputs the enumerated pathways (using `EC numbers <https://en.wikipedia.org/wiki/Enzyme_Commission_number>`_ ) as well as the structure of involved chemicals (as SMILES: Simplified Molecular-Input Line-Entry System) in TSV format.
+
+
+An example of **enumerated pathways** is illustred in the figure below for the production of a target molecule: `Styrene <https://en.wikipedia.org/wiki/Styrene>`_. **Compounds** are represented by their structures, and **reactions** by their `EC numbers <https://en.wikipedia.org/wiki/Enzyme_Commission_number>`_.
+
+
+.. image:: ${static_path}/images/enumerated_pathways.png
+    :width: 40 %
+    :align: center
+
+|
+
+Input
+-----
+
+Required information:
+
+* **RetroPath2.0 Pathways**\ : Retrosynthesis network CSV file outputted by the RetroPath2 tool which desribes the network linking the targeted compound to the chassis.
+
+Advanced options:
+
+* **Time Out**\ : (integer) Timeout before killing a process (in seconds), default: 30 minutes.
+
+Output
+------
+
+* **Enumerated Pathways**\ : Describes all the indiviudal enumerated pathways that produce the compound of interest.
+* **Compounds**\ : Describes the structure of all the chemical species involved in all pathways as SMILES (Simplified Molecular-Input Line-Entry System).
+
+Project Links
+---------------------
+
+* `GitHub <https://github.com/brsynth/rp2paths>`_
+
+License
+-------
+
+`MIT <https://github.com/brsynth/rp2paths/blob/master/LICENSE.md>`_
+
+Acknowledgments
+---------------
+
+* Joan Hérisson
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1016/j.ymben.2017.12.002</citation>
+    </citations>
+</tool>
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