comparison featurecounts.xml @ 17:8ce1e2c7ee72 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018

16:92808b865dfb

<tool id="featurecounts" name="featureCounts" version="1.6.0.6" profile="16.04">
    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
    <requirements>
        <requirement type="package" version="1.6.0">subread</requirement>
    </requirements>

    <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
    <command detect_errors="exit_code"><![CDATA[

            --fracOverlap $extended_parameters.frac_overlap
            --fracOverlapFeature $extended_parameters.frac_overlap_feature
                $extended_parameters.read_reduction
                $extended_parameters.primary
                $extended_parameters.ignore_dup

                #if str($extended_parameters.read_extension_5p) != "0":
                    --readExtension5 $extended_parameters.read_extension_5p
                #end if

                #if str($extended_parameters.read_extension_3p) != "0":

        #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

        && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
    ]]></command>
    <inputs>
        <param name="alignment"
               type="data"

                   falsevalue=""
                   argument="--ignoreDup"
                   label="Ignore reads marked as duplicate"
                   help="If specified, reads that were marked as duplicates will be ignored. Bit Ox400 in the FLAG field of a SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read." />

            <param name="count_split_alignments_only"
                   type="boolean"
                   truevalue=" --countSplitAlignmentsOnly"
                   falsevalue=""
                   argument="--countSplitAlignmentsOnly"

            <actions>
                <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length" />
            </actions>
        </data>

        <data format="tabular"
              name="output_short"
              label="${tool.name} on ${on_string}">
            <filter>format == "tabdel_short"</filter>
            <actions>

            <output name="output_jcounts" file="output_1_jcounts.tab">
                <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/>
            </output>
        </test>
        <!-- Ensure featureCounts built-in annotation works -->
        <test expect_num_outputs="2">
            <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19" />
            <param name="anno_select" value="builtin"/>
            <param name="format" value="tabdel_short" />
            <output name="output_short" file="output_builtin_hg19.tab">
                <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            </output>
            <output name="output_summary" file="output_summary_builtin_hg19.tab"/>
        </test>
        <!-- Ensure cached GTFs work -->
        <test expect_num_outputs="3">
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />
            <param name="anno_select" value="cached"/>

17:8ce1e2c7ee72

<tool id="featurecounts" name="featureCounts" version="1.6.0.7" profile="16.04">
    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
    <requirements>
        <requirement type="package" version="1.6.0">subread</requirement>
        <requirement type="package" version="1.7">samtools</requirement>
    </requirements>

    <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
    <command detect_errors="exit_code"><![CDATA[

            --fracOverlap $extended_parameters.frac_overlap
            --fracOverlapFeature $extended_parameters.frac_overlap_feature
                $extended_parameters.read_reduction
                $extended_parameters.primary
                $extended_parameters.ignore_dup
                #if $extended_parameters.R:
                    $extended_parameters.R
                #end if
                #if str($extended_parameters.read_extension_5p) != "0":
                    --readExtension5 $extended_parameters.read_extension_5p
                #end if

                #if str($extended_parameters.read_extension_3p) != "0":

        #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"
               type="data"

                   falsevalue=""
                   argument="--ignoreDup"
                   label="Ignore reads marked as duplicate"
                   help="If specified, reads that were marked as duplicates will be ignored. Bit Ox400 in the FLAG field of a SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read." />

            <param type="boolean"
                   truevalue="-R BAM"
                   falsevalue=""
                   argument="-R"
                   label="Annotates the alignment file with 'XS:Z:'-tags to described per read or read-pair the corresponding assigned feature(s)."
                   help="" />

            <param name="count_split_alignments_only"
                   type="boolean"
                   truevalue=" --countSplitAlignmentsOnly"
                   falsevalue=""
                   argument="--countSplitAlignmentsOnly"

            <actions>
                <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length" />
            </actions>
        </data>

        <data format="bam"
              name="output_bam"
              label="${tool.name} on ${on_string}: Alignment file">
            <filter>extended_parameters['R']</filter>
        </data>

        <data format="tabular"
              name="output_short"
              label="${tool.name} on ${on_string}">
            <filter>format == "tabdel_short"</filter>
            <actions>

            <output name="output_jcounts" file="output_1_jcounts.tab">
                <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/>
            </output>
        </test>
        <!-- Ensure featureCounts built-in annotation works -->
        <test expect_num_outputs="3">
            <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19" />
            <param name="anno_select" value="builtin"/>
            <param name="format" value="tabdel_short" />
            <section name="extended_parameters">
                <param name="R" value="true" />
            </section>
            <output name="output_short" file="output_builtin_hg19.tab">
                <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            </output>
            <output name="output_summary" file="output_summary_builtin_hg19.tab"/>
            <output name="output_bam" file="output.bam" ftype="bam"/>
        </test>
        <!-- Ensure cached GTFs work -->
        <test expect_num_outputs="3">
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />
            <param name="anno_select" value="cached"/>