comparison featurecounts.xml @ 27:ce44c6f2ba38 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c2db6daac834eea9b88388aed840d484544f0786"

26:ea04b737afa0

<tool id="featurecounts" name="featureCounts" version="2.0.1" profile="16.04">
    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
    <requirements>
        <requirement type="package" version="2.0.1">subread</requirement>
        <requirement type="package" version="1.11">samtools</requirement>
        <requirement type="package" version="8.31">coreutils</requirement>
    </requirements>

    <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>

        #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
            && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}'
        #end if

        #if $extended_parameters.R:
            && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam
        #end if
        && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
    ]]></command>
    <inputs>
        <param name="alignment"

27:ce44c6f2ba38

<tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
    <macros>
        <token name="@TOOL_VERSION@">2.0.1</token>
        <token name="@VERSION_SUFFIX@">1</token>
    </macros>

    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">subread</requirement>
        <requirement type="package" version="1.11">samtools</requirement>
        <requirement type="package" version="8.31">coreutils</requirement>
    </requirements>

    <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>

        #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
            && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}'
        #end if

        #if $extended_parameters.R:
            && samtools sort --no-PG -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam
        #end if
        && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
    ]]></command>
    <inputs>
        <param name="alignment"