comparison featurecounts.xml @ 24:a37612abf7f9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 809715c88721d082b304cf4e4a37b52d30162f08"

23:9301937c9037

<tool id="featurecounts" name="featureCounts" version="1.6.4" profile="16.04">
    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
    <requirements>
        <requirement type="package" version="1.6.4">subread</requirement>
        <requirement type="package" version="1.9">samtools</requirement>
        <requirement type="package" version="8.31">coreutils</requirement>

        #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} *.featureCounts.bam
        #end if
        && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
    ]]></command>
    <inputs>
        <param name="alignment"

                <option value="history">in your history</option>
            </param>
            <when value="builtin">
                <param name="bgenome" type="select" label="Select built-in genome" help="Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts">
                    <options from_data_table="featurecounts_anno">
                        <filter type="data_meta" key="dbkey" ref="alignment" column="0"/>
                    </options>
                </param>
            </when>
            <when value="cached">
                <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator">
                    <options from_data_table="gene_sets">
                        <filter type="data_meta" key="dbkey" ref="alignment" column="0"/>
                    </options>
                    <validator type="no_options" message="An annotation file is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">

24:a37612abf7f9

<tool id="featurecounts" name="featureCounts" version="1.6.4+galaxy1" profile="16.04">
    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
    <requirements>
        <requirement type="package" version="1.6.4">subread</requirement>
        <requirement type="package" version="1.9">samtools</requirement>
        <requirement type="package" version="8.31">coreutils</requirement>

        #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"

                <option value="history">in your history</option>
            </param>
            <when value="builtin">
                <param name="bgenome" type="select" label="Select built-in genome" help="Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts">
                    <options from_data_table="featurecounts_anno">
                        <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
                    </options>
                </param>
            </when>
            <when value="cached">
                <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator">
                    <options from_data_table="gene_sets">
                        <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
                        <filter type="sort_by" column="2" />
                    </options>
                    <validator type="no_options" message="An annotation file is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">