comparison retropath2.xml @ 2:8a04f97b785d draft

"planemo upload commit 2f1af427fa4c4f2aad53ab94c4cdb51456c66019-dirty"

1:d3f66245c4a6

<tool id="retropath2" name="RetroPath2.0" version="2.0.5">
    <description>Build a reaction network from a set of source compounds to a set of sink compounds</description>
    <requirements>
        <requirement type="package" version="2.0.5">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" />

    <command detect_errors="exit_code"><![CDATA[
        python -m retropath2_wrapper
            '$sinkfile'
            '$rulesfile'
            out
            --source_inchi '$source_inchi'
            #if $source_name:
                --source_name '$source_name'
            #end if
            --max_steps '$adv.max_steps'
            --topx '$adv.topx'
            --dmin '$adv.dmin'
            --dmax '$adv.dmax'
            --mwmax_source '$adv.mwmax_source'

        else
            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="source_inchi" type="text"       label="Source InChI"     optional="false"    >
            <validator type="empty_field" message="You must provide the InChI key" />
        </param>
        <param name="source_name"  type="text" value="target" optional="true" label="Source name"         />
        <section name="adv" title="Advanced Options" expanded="false">
            <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)" />

Input
-----

Required:


* **-sinkfile**\ : (string) Path to the sink file
* **-sourcefile**\ : (string) Path to the source file
* **-max_steps**\ : (integer) Maximal number of steps
* **-rulesfile**\ : (string) Path to the rules file
* **-rulesfile_format**\ : (string) Valid Options: tar, csv. Format of the rules file

Advanced options:


* **-topx**\ : (integer, default: 100) For each iteration, number of rules
* **-dmin**\ : (integer, default: 0)
* **-dmax**\ : (integer, default: 1000)
* **-mwmax_source**\ : (integer, default: 1000)

* **-timeout**\ : (integer, default: 30) Timeout in minutes

Output
------


* **-scope_csv**\ : (string) Path to the output scope csv file

Version
-------

v2.0.4

Authors
-------


* **Melchior du Lac**
* Joan Hérisson

License
-------

This project is licensed under the MIT License.

Acknowledgments
---------------


* Thomas Duigou

    ]]></help>
    <citations>

2:8a04f97b785d

<tool id="retropath2" name="RetroPath2.0" version="2.3.0">
    <description>Build a reaction network from a set of source compounds to a set of sink compounds</description>
    <requirements>
        <requirement type="package" version="2.3.0">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" />

    <command detect_errors="exit_code"><![CDATA[
        python -m retropath2_wrapper
            '$sinkfile'
            '$rulesfile'
            out
            --source_inchi '$source_inchi_type.source_inchi'
            --source_name '$source_name'
            --rp2_version '$adv.version'
            --max_steps '$adv.max_steps'
            --topx '$adv.topx'
            --dmin '$adv.dmin'
            --dmax '$adv.dmax'
            --mwmax_source '$adv.mwmax_source'

        else
            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"/>
        <conditional name="source_inchi_type">
            <param name="inchi_type" type="select" label="InChI type">
                <!-- <option value="name" selected="true">By name</option> -->
                <option value="string">By string</option>
            </param>
            <when value="string">
                <param name="source_inchi" type="text" label="Source InChI" optional="false">
                    <validator type="empty_field" message="You must provide the InChI string"/>
                </param>
            </when>
        </conditional>
        <param name="source_name" type="text" value="target" optional="true" label="Source name"/>
        <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)" />

Input
-----

Required:

* **-sinkfile**\ : (string) Path to the sink file
* **-sourcefile**\ : (string) Path to the source file
* **-max_steps**\ : (integer) Maximal number of steps
* **-rulesfile**\ : (string) Path to the rules file
* **-rulesfile_format**\ : (string) Valid Options: tar, csv. Format of the rules file

The InChI source DB entries are obtained by the following command:

`cat chem_prop.tsv | awk -F'\\t' '{print "\\t\\t\\t\\t\\t<option value=\\""$6"\\"\\>" "["$1"]\\t " $2 "</option>"}' | sed 's/\\&/\\&amp;/g'`

where `chem_prop.tsv` has been downloaded on MetaNetX.

Advanced options:

* **-topx**\ : (integer, default: 100) For each iteration, number of rules
* **-dmin**\ : (integer, default: 0)
* **-dmax**\ : (integer, default: 1000)
* **-mwmax_source**\ : (integer, default: 1000)

* **-timeout**\ : (integer, default: 30) Timeout in minutes

Output
------

* **-scope_csv**\ : (string) Path to the output scope csv file

Authors
-------

* **Joan Hérisson**
* Melchior du Lac

License
-------

This project is licensed under the MIT License.

Acknowledgments
---------------

* Thomas Duigou

    ]]></help>
    <citations>