comparison obisort.xml @ 3:e614dcabd870 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"

2:12b9e285ca1c

<tool id="obi_sort" name="obisort" version="@TOOL_VERSION@">
    <description>sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>

    <command>

        <![CDATA[
            obisort
            -k '$key'
            ${reverse}
            '$input' > '$output'
        ]]>

    </command>

    <inputs>
        <param name="input" type="data" format="fastq,fasta,txt,tabular" label="Input sequences file" />
        <param name="key" type="text" label="key" />
        <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="sorts in reverse order?" />
        <param name="out_format" type="select" label="Output data type">
            <option value="fasta">fasta</option>
            <option value="fastq">fastq</option>
        </param>

    </inputs>
    <outputs>
        <data format="fastq" name="output" label="output with ${tool.name} on ${on_string}" >
            <change_format>
                <when input="out_format" value="fasta" format="fasta" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="output_obiclean_advanced.fasta" />
            <param name="key" value="count"/>

        <test>
            <param name="input" value="output_obiclean_advanced.fasta" />
            <param name="key" value="count"/>
            <param name="reverse" value="True"/>
            <param name="out_format" value="fastq"/>
            <output name="output" file="output_obisort.fastq" ftype="fastq"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

3:e614dcabd870

<tool id="obi_sort" name="obisort" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>sorts sequence records according to the value of a given attribute</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>

    <command><![CDATA[
        @GUNZIP_INPUT@
        obisort
        --without-progress-bar
        -k '$key'
        ${reverse}
        @INPUT_FORMAT@
        @OUT_FORMAT@
        input
        @GZIP_OUTPUT@
        > '$output'
        @GENERATE_GALAXY_JSON@
    ]]></command>
    <inputs>
        <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" />
        <param name="key" type="text" label="key"/>
        <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="sorts in reverse order?" />
        <expand macro="input_format_options_macro"/>
        <expand macro="out_format_macro"/>
    </inputs>
    <outputs>
        <data format="auto" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="output_obiclean_advanced.fasta" />
            <param name="key" value="count"/>

        <test>
            <param name="input" value="output_obiclean_advanced.fasta" />
            <param name="key" value="count"/>
            <param name="reverse" value="True"/>
            <param name="out_format" value="fastq"/>
            <output name="output" file="output_obisort.fastq" ftype="fastqsanger"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark