comparison dexseq_count.xml @ 10:df929f257179 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 2ea27822b171dbf519509dc1da150c8ccee2a140

9:b47c006d90c5

<tool id="dexseq_count" name="DEXSeq-Count" version="@TOOL_VERSION@.1" profile="@PROFILE@">
    <description>Prepare and count exon abundancies from RNA-seq data</description>
    <xrefs>
        <xref type="bio.tools">dexseq</xref>
    </xrefs>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
    </expand>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <!-- In case the return code has not been set propery check stderr too -->

        --minaqual $mode.qual
        --order $mode.order
        $mode.flattened_gtf_in
        '$mode.bamfile'
        '$counts_file'
#end if
    ]]></command>
    <inputs>
        <conditional name="mode">
            <param name="mode_select" type="select" label="Mode of operation">

10:df929f257179

<tool id="dexseq_count" name="DEXSeq-Count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Prepare and count exon abundancies from RNA-seq data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements"/>
    <stdio>
        <!-- Anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
        <!-- In case the return code has not been set propery check stderr too -->

        --minaqual $mode.qual
        --order $mode.order
        $mode.flattened_gtf_in
        '$mode.bamfile'
        '$counts_file'
    &&
    sed -i 's/\"//g' '$counts_file'
#end if
    ]]></command>
    <inputs>
        <conditional name="mode">
            <param name="mode_select" type="select" label="Mode of operation">