comparison featurecounts.xml @ 14:85aaf50ad9dc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 650fa1433cf8fbc8689ed35a4d0340fc7a130aca

13:386220cf6877

<tool id="featurecounts" name="featureCounts" version="1.6.0.5" 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>

            #end if

            -o "output"
            -T \${GALAXY_SLOTS:-2}

            -t '$extended_parameters.gff_feature_type'
            -g '$extended_parameters.gff_feature_attribute'
                $extended_parameters.summarization_level
                $extended_parameters.contribute_to_multiple_features
            -s  $extended_parameters.strand_specificity
                $extended_parameters.multimapping_enabled.multimapping_counts

                #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M":
                    $extended_parameters.multimapping_enabled.fraction
                #end if

               type="data"
               multiple="false"
               format="bam,sam"
               label="Alignment file"
               help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format. Unless you are using a Gene annotation file from the History, these files must have the database/genome attribute already specified e.g. hg38, not the default: ?" >
        </param>

        <conditional name="anno">
            <param name="anno_select" type="select" label="Gene annotation file">
                <option value="builtin">featureCounts built-in</option>

                falsevalue=""
                argument="-O"
                label="Allow read to contribute to multiple features"
                help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta-feature (or matched feature if -f is specified)" />

            <param name="strand_specificity"
                   type="select"
                   label="Strand specificity of the protocol"
                   argument="-s"
                   help="Indicate if strand-specific read counting should be performed.">
                <option value="0" selected="true">Unstranded</option>
                <option value="1">Stranded (forwards)</option>
                <option value="2">Stranded (reverse)</option>
            </param>

            <conditional name="multimapping_enabled">
                <param name="multimapping_counts"
                       type="select"
                       argument="-M"
                       label="Count multi-mapping reads/fragments"

Annotations for gene regions should be provided in the GFF/GTF format:

 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
 - http://www.ensembl.org/info/website/upload/gff.html

Alternatively, the featureCounts built-in annotations for genomes hg38, hg19, mm10 and mm9 can be used through selecting the built-in option above. These annotations were downloaded from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene. See the Subread_ User's Guide for more information.

Output format
-------------
FeatureCounts produces a table containing counted reads, per gene, per row. Optionally the last column can be set to be the effective gene-length. These tables are compatible with the DESeq2, edgeR and limma-voom Galaxy wrappers by IUC.

.. _Subread: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btt656</citation>
    </citations>
</tool>

14:85aaf50ad9dc

<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>

            #end if

            -o "output"
            -T \${GALAXY_SLOTS:-2}

            -s  $strand_specificity
            -t '$extended_parameters.gff_feature_type'
            -g '$extended_parameters.gff_feature_attribute'
                $extended_parameters.summarization_level
                $extended_parameters.contribute_to_multiple_features
                $extended_parameters.multimapping_enabled.multimapping_counts

                #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M":
                    $extended_parameters.multimapping_enabled.fraction
                #end if

               type="data"
               multiple="false"
               format="bam,sam"
               label="Alignment file"
               help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format. Unless you are using a Gene annotation file from the History, these files must have the database/genome attribute already specified e.g. hg38, not the default: ?" >
        </param>

        <param name="strand_specificity"
               type="select"
               label="Specify strand information"
               argument="-s"
               help="Indicate if the data is stranded and if strand-specific read counting should be performed. Strand setting must be the same as the strand settings used to produce the mapped BAM input(s)">
            <option value="0" selected="true">Unstranded</option>
            <option value="1">Stranded (Forward)</option>
            <option value="2">Stranded (Reverse)</option>
        </param>

        <conditional name="anno">
            <param name="anno_select" type="select" label="Gene annotation file">
                <option value="builtin">featureCounts built-in</option>

                falsevalue=""
                argument="-O"
                label="Allow read to contribute to multiple features"
                help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta-feature (or matched feature if -f is specified)" />

            <conditional name="multimapping_enabled">
                <param name="multimapping_counts"
                       type="select"
                       argument="-M"
                       label="Count multi-mapping reads/fragments"

Annotations for gene regions should be provided in the GFF/GTF format:

 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
 - http://www.ensembl.org/info/website/upload/gff.html

Alternatively, the featureCounts built-in annotations for genomes hg38, hg19, mm10 and mm9 can be used through selecting the built-in option above. These annotation files are in simplified annotation format (SAF) as shown below. The GeneID column contains Entrez gene identifiers and each entry (row) is taken as a feature (e.g. an exon).

Example - **Built-in annotation format**:

  ======  ====  =======  =======  ======
  GeneID  Chr   Start    End      Strand
  ======  ====  =======  =======  ======
  497097  chr1  3204563  3207049  -
  497097  chr1  3411783  3411982  -
  497097  chr1  3660633  3661579  -
  ======  ====  =======  =======  ======

These annotation files can be found in the `Subread package`_. You can see the version of Subread used by this wrapper in the tool form above under `Options > Requirements`. To create the files, the annotations were downloaded from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene. See the `Subread User's Guide`_ for more information.

Output format
-------------
FeatureCounts produces a table containing counted reads, per gene, per row. Optionally the last column can be set to be the effective gene-length. These tables are compatible with the DESeq2, edgeR and limma-voom Galaxy wrappers by IUC.

.. _Subread: http://subread.sourceforge.net/
.. _`Subread User's Guide`: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
.. _`Subread package`: https://sourceforge.net/projects/subread/files/
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btt656</citation>
    </citations>
</tool>