comparison rrparser.xml @ 5:d7882cf07d98 draft

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

4:3f39c7d3c14e

<tool id="rrparser" name="RRules Parser" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
    <description>Retrieve the reaction rules from RetroRules</description>
    <macros>
        <token name="@VERSION_SUFFIX@">0</token>
        <token name="@TOOL_VERSION@">2.4.6</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
    </requirements>
    <stdio>

        <regex match="ERROR:" level="fatal" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        python -m rrparser
        #if str($rules.type) != "rules-file":
            retrorules
            --rule-type '$rules.type'
        #else:
            '$rules.file'
            --input-format '$rules.input_format'
        #end if
        --diameters '$diameters'
        --output-format csv
        #if str($compress) == "true":
            --outfile '$out_rules'.csv.gz
            && mv '$out_rules'.csv.gz '$out_rules'
        #else:
            --outfile '$out_rules'

                <option value="retro" selected="True">RetroRules (retro)</option>
                <option value="forward">RetroRules (forward)</option>
                <option value="all">RetroRules (all)</option>
                <option value="rules-file">Other reaction rules...</option>
            </param>
            <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)">
                    <option value="csv" selected="True">csv</option>
                    <option value="tsv">tsv</option>

Ouput
-----

* **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>
    <citations>
        <citation type="doi">10.1093/nar/gky940 </citation>
    </citations>
</tool>

5:d7882cf07d98

<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@">2.5.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rrparser</requirement>
    </requirements>
    <stdio>

        <regex match="ERROR:" level="fatal" />
    </stdio>
    <command detect_errors="exit_code"><![CDATA[
        python -m rrparser
        #if str($rules.type) != "rules-file":
            --rules_file retrorules
            --rule-type '$rules.type'
        #else:
            --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 '$out_rules'
        #else:
            --outfile '$out_rules'

                <option value="retro" selected="True">RetroRules (retro)</option>
                <option value="forward">RetroRules (forward)</option>
                <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)">
                    <option value="csv" selected="True">csv</option>
                    <option value="tsv">tsv</option>

Ouput
-----

* **out_rules**: (string): file containing the parsed reactions rules (default=csv). It will be zipped if *Compress output* is set to yes.
    ]]></help>
    <creator>
        <organization name="BioRetroSynth" url="https://github.com/brsynth"/>
    </creator>
    <citations>
        <citation type="doi">10.1093/nar/gky940</citation>
    </citations>
</tool>