comparison featurecounts.xml @ 20:1759d845181e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit c8c08f052bdffcbfd14eebd760af923486bcf8c5

19:f3a5f075498f

<tool id="featurecounts" name="featureCounts" version="1.6.2" profile="16.04">
    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
    <requirements>
        <requirement type="package" version="1.6.2">subread</requirement>
        <requirement type="package" version="1.7">samtools</requirement>
    </requirements>

        </section>
    </inputs>
    <outputs>
        <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>

            <filter>extended_parameters['R']</filter>
        </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"
              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"
              label="${tool.name} on ${on_string}: feature lengths">
            <filter>include_feature_length_file</filter>
            <actions>
                <action name="column_names" type="metadata" default="Feature,Length" />
            </actions>
        </data>

        <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>

20:1759d845181e

<tool id="featurecounts" name="featureCounts" version="1.6.3" profile="16.04">
    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
    <requirements>
        <requirement type="package" version="1.6.2">subread</requirement>
        <requirement type="package" version="1.7">samtools</requirement>
    </requirements>

        </section>
    </inputs>
    <outputs>
        <data format="tabular"
              name="output_medium"
              label="${tool.name} on ${on_string}: Counts (with length)">
            <filter>format == "tabdel_medium"</filter>
            <actions>
                <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length" />
            </actions>
        </data>

            <filter>extended_parameters['R']</filter>
        </data>

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

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

        <data format="tabular"
              name="output_summary"
              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"
              label="${tool.name} on ${on_string}: Feature lengths">
            <filter>include_feature_length_file</filter>
            <actions>
                <action name="column_names" type="metadata" default="Feature,Length" />
            </actions>
        </data>

        <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>