comparison featurecounts.xml @ 9:e6a2a912677a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4fb528145289ad4db04e4589c02e9ddaa1194138

8:2a8bb8223a45

<tool id="featurecounts" name="featureCounts" version="1.6.0" 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>

        <data format="tabular"
              name="output_medium"
              label="${tool.name} on ${on_string}">
            <filter>format == "tabdel_medium"</filter>
            <actions>
                <action name="column_names" type="metadata" default="Geneid,${alignment.name},Length" />
            </actions>
        </data>

        <data format="tabular"
              name="output_short"
              label="${tool.name} on ${on_string}">
            <filter>format == "tabdel_short"</filter>
            <actions>
                <action name="column_names" type="metadata" default="Geneid,${alignment.name}" />
            </actions>
        </data>

        <data format="tabular"
              name="output_full"
              label="${tool.name} on ${on_string}: count table">
            <filter>format == "tabdel_full"</filter>
            <actions>
                <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.name}" />
            </actions>
        </data>

        <data format="tabular"
              name="output_summary"
              hidden="true"
              label="${tool.name} on ${on_string}: summary">
            <actions>
                <action name="column_names" type="metadata" default="Status,${alignment.name}" />
            </actions>
        </data>

        <data format="tabular"
              name="output_feature_lengths"

        <data name="output_jcounts" format="tabular"
              label="${tool.name} on ${on_string}: junction counts">
            <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter>
            <actions>
                <action name="column_names" type="metadata" default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.name}" />
            </actions>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="4">

9:e6a2a912677a

<tool id="featurecounts" name="featureCounts" version="1.6.0.1" 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>

        <data format="tabular"
              name="output_medium"
              label="${tool.name} on ${on_string}">
            <filter>format == "tabdel_medium"</filter>
            <actions>
                <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length" />
            </actions>
        </data>

        <data format="tabular"
              name="output_short"
              label="${tool.name} on ${on_string}">
            <filter>format == "tabdel_short"</filter>
            <actions>
                <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier}" />
            </actions>
        </data>

        <data format="tabular"
              name="output_full"
              label="${tool.name} on ${on_string}: count table">
            <filter>format == "tabdel_full"</filter>
            <actions>
                <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.element_identifier}" />
            </actions>
        </data>

        <data format="tabular"
              name="output_summary"
              hidden="true"
              label="${tool.name} on ${on_string}: summary">
            <actions>
                <action name="column_names" type="metadata" default="Status,${alignment.element_identifier}" />
            </actions>
        </data>

        <data format="tabular"
              name="output_feature_lengths"

        <data name="output_jcounts" format="tabular"
              label="${tool.name} on ${on_string}: junction counts">
            <filter>extended_parameters['exon_exon_junction_read_counting_enabled']['count_exon_exon_junction_reads']</filter>
            <actions>
                <action name="column_names" type="metadata" default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.element_identifier}" />
            </actions>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="4">