comparison featurecounts.xml @ 7:3ce1c701b0df draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a705dfd329f2e917d549215715385f5ef5001d17

6:9d60a36b5c6a

                    $extended_parameters.multimapping_enabled.fraction
                #end if

                $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
                #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J"
                    -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome'
                #end if

                $extended_parameters.long_reads

            -Q  $extended_parameters.mapping_quality

            <conditional name="exon_exon_junction_read_counting_enabled">
                <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue=""
                       label="Exon-exon junctions"
                       help="If specified, reads supporting each exon-exon junction will be counted" />
                <when value="-J">
                    <param name="genome" argument="-G" type="data" format="fasta"
                           label="Reference sequence (genome) file"
                           help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions" />
                </when>
                <when value="" />
            </conditional>

            </actions>
        </data>

        <data name="output_jcounts" format="tabular"
              label="${tool.name} on ${on_string}: junction counts">
            <filter>extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads == " -J"</filter>
            <actions>
                <action name="column_names" type="metadata" default="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,${alignment.name}" />
            </actions>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_short" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />
            <output name="output_short" file="output_1_short.tab">
                <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
            </output>
            <output name="output_summary" file="output_1_summary.tab"/>
        </test>
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_medium" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />

            </output>
            <output name="output_summary" file="output_1_summary.tab">
                <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
            </output>
        </test>
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_full" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />

            <output name="output_feature_lengths" file="output_feature_lengths.tab">
                <metadata name="column_names" value="Feature,Length"/>
            </output>
        </test>
        
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_short" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />
            <output name="output_short" file="output_2_short.tab">
                <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
            </output>
            <output name="output_summary" file="output_2_summary.tab">
                <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
            </output>
        </test>
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_medium" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />
            <output name="output_medium" file="output_2_medium.tab">
                <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
            </output>
            <output name="output_summary" file="output_2_summary.tab">
                <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
            </output>
        </test>
        <test>
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_full" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />
            <output name="output_full" file="output_2_full.tab">
                <metadata name="column_names" value="Geneid,Chr,Start,End,Strand,Length,featureCounts_input1.bam"/>
            </output>
            <output name="output_summary" file="output_2_summary.tab">
                <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
            </output>
            <output name="output_feature_lengths" file="output_feature_lengths.tab">
                <metadata name="column_names" value="Feature,Length"/>
            </output>
        </test>
    </tests>
    
    <help><![CDATA[
featureCounts
#############

7:3ce1c701b0df

                    $extended_parameters.multimapping_enabled.fraction
                #end if

                $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
                #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J"
                    #if $extended_parameters.exon_exon_junction_read_counting_enabled.genome
                        -G '$extended_parameters.exon_exon_junction_read_counting_enabled.genome'
                    #end if
                #end if

                $extended_parameters.long_reads

            -Q  $extended_parameters.mapping_quality

            <conditional name="exon_exon_junction_read_counting_enabled">
                <param name="count_exon_exon_junction_reads" argument="-J" type="boolean" truevalue="-J" falsevalue=""
                       label="Exon-exon junctions"
                       help="If specified, reads supporting each exon-exon junction will be counted" />
                <when value="-J">
                    <param name="genome" argument="-G" type="data" format="fasta" optional="true"
                           label="Reference sequence file"
                           help="The FASTA-format file that contains the reference sequences used in read mapping can be used to improve read counting for junctions" />
                </when>
                <when value="" />
            </conditional>

            </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.name}" />
            </actions>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="4">
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_short" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />
            <param name="count_exon_exon_junction_reads" value="-J"/>
            <output name="output_short" file="output_1_short.tab">
                <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
            </output>
            <output name="output_summary" file="output_1_summary.tab">
                <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
            </output>
            <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>
        <test expect_num_outputs="3">
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_medium" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />

            </output>
            <output name="output_summary" file="output_1_summary.tab">
                <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
            </output>
        </test>
        <test expect_num_outputs="3">
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_full" />
            <param name="include_feature_length_file" value="true"/>
            <param name="ref_source" value="history" />

            <output name="output_feature_lengths" file="output_feature_lengths.tab">
                <metadata name="column_names" value="Feature,Length"/>
            </output>
        </test>
        
    </tests>
    
    <help><![CDATA[
featureCounts
#############