comparison featurecounts.xml @ 10:46cccc52be5f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit cf1ae941d02bff8848f05c4e4039457656e3a4e8

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>

    <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
    <command><![CDATA[
        ## Check whether all alignments are from the same type (bam || sam)
        featureCounts
            #if $gtf_source.ref_source=="history":
                -a '$gtf_source.reference_gene_sets'
            #else:
                -a '$gtf_source.reference_gene_sets_builtin.fields.path'
            #end if

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

                $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

                $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
                #if str($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

            --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"
                    --readExtension3 $extended_parameters.read_extension_3p
                #end if

                $pe_parameters.fragment_counting_enabled.fragment_counting
                #if str($pe_parameters.fragment_counting_enabled.fragment_counting) == " -p"
                    $pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance
                    #if str($pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance) == " -P"
                        -d $pe_parameters.fragment_counting_enabled.check_distance_enabled.minimum_fragment_length
                        -D $pe_parameters.fragment_counting_enabled.check_distance_enabled.maximum_fragment_length
                    #end if
                #end if

                $pe_parameters.only_both_ends
                $pe_parameters.exclude_chimerics

        '${alignment}'

        ## Removal of comment and column-header line
        && grep -v "^#" "output" | tail -n+2 > body.txt

        ## Set the right columns for the tabular formats
        #if $format.value == "tabdel_medium"
            && cut -f 1,7 body.txt > expression_matrix.txt

            ## Paste doesn't allow a non ordered list of columns: -f 1,7,8,6 will only return columns 1,7 and 8
            ## Thus the gene length column (last column) has to be added separately
            && cut -f 6 body.txt > gene_lengths.txt
            && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak
            && mv -f expression_matrix.txt.bak '${output_medium}'
        #elif $format.value == "tabdel_short"
            && cut -f 1,7 body.txt > '${output_short}'
        #else
            && cp body.txt '${output_full}'
        #end if


        #if str($include_feature_length_file) == "true"
            && cut -f 1,6 body.txt > '${output_feature_lengths}'
        #end if

        #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J"
            && tail -n+2 'output.jcounts' > '${output_jcounts}'
        #end if

        && tail -n+2 'output.summary' > '${output_summary}'

    ]]></command>
    <inputs>
        <param name="alignment"
               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" />

        <conditional name="gtf_source">
            <param name="ref_source" type="select" label="Gene annotation file">
                <option value="cached">locally cached</option>
                <option value="history">in your history</option>
            </param>
            <when value="cached">
                <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator">
                    <options from_data_table="gene_sets">
                        <filter type="sort_by" column="1" />
                        <validator type="no_options" message="No annotations are available." />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="reference_gene_sets"
                       format="gff,gtf,gff3"
                       type="data"
                       label="Gene annotation file"
                       help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment" />
            </when>
        </conditional>

        <param name="format"
               type="select"
               label="Output format"
               help="The output format will be tabular, select the preferred columns here">
            <option value="tabdel_short" selected="true">Gene-ID "\t" read-count (DESeq2 IUC wrapper compatible)</option>
            <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option>
            <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option>
        </param>

        <param name="include_feature_length_file"

            <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue=""
                   label="Long reads"
                   help="If specified, long reads such as Nanopore and PacBio reads will be counted. Long read counting can only run in one thread and only reads (not read-pairs) can be counted." />

           <param name="by_read_group" argument="--byReadGroup" type="boolean" truevalue="--byReadGroup" falsevalue=""
                  label="Count reads by read group"
                  help="If specified, reads are counted for each read group separately. The 'RG' tag must be present in the input BAM/SAM alignment files." />


            <param name="largest_overlap"

                   value="1"
                   argument="--minOverlap"
                   label="Minimum bases of overlap"
                   help="Specify the minimum required number of overlapping bases between a read (or a fragment) and a feature. 1 by default. If a negative value is provided, the read will be extended from both ends." />

           <param name="frac_overlap"
                  type="integer"
                  value="0"
                  min="0"
                  max="1"
                  argument="--fracOverlap"
                  label="Minimum fraction (of read) overlapping a feature"
                  help="Specify the minimum required fraction of overlapping bases between a read (or a fragment) and a feature. Value should be within range [0,1]. 0 by default. Number of overlapping bases is counted from both reads if paired end. Both this option and '--minOverlap' need to be satisfied for read assignment." />

              <param name="frac_overlap_feature"
                     type="integer"
                     value="0"
                     min="0"
                     max="1"
                     argument="--fracOverlapFeature"

        </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>

            </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 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">
            <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"/>

                <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 name="output_medium" file="output_1_medium.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_full" file="output_1_full.tab">

            </output>
            <output name="output_feature_lengths" file="output_feature_lengths.tab">
                <metadata name="column_names" value="Feature,Length"/>
            </output>
        </test>

    </tests>

    <help><![CDATA[
featureCounts
#############

Overview
--------
FeatureCounts is a light-weight read counting program written entirely in the C programming language. It can be used to count both gDNA-seq and RNA-seq reads for genomic features in in SAM/BAM files.

Input formats
-------------
Alignments should be provided in either:

 - SAM format, http://samtools.sourceforge.net/samtools.shtml#5
 - BAM format

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

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 Galaxy wrapper by IUC. Column names are added as metadata object.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btt656</citation>
    </citations>
</tool>

10:46cccc52be5f

<tool id="featurecounts" name="featureCounts" version="1.6.0.2" profile="16.04">
    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
    <requirements>
        <requirement type="package" version="1.6.0">subread</requirement>
    </requirements>

    <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
    <command detect_errors="exit_code"><![CDATA[
        ## Export fc path for its built-in annotation
        export FC_PATH=\$(command -v featureCounts | sed 's@/bin/featureCounts$@@') &&

        ## Check whether all alignments are from the same type (bam || sam)
        featureCounts

            #if $anno.anno_select=="gtf":
                #if $anno.gtf_source.ref_source=="history":
                    -a '$anno.gtf_source.reference_gene_sets'
                #else:
                    -a '$anno.gtf_source.reference_gene_sets_builtin.fields.path'
                #end if
                -F "GTF"
            #elif $anno.anno_select=="builtin":
                -a \${FC_PATH}/annotation/${anno.genome}_RefSeq_exon.txt
                -F "SAF"
            #end if

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

                $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

                $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
                #if str($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

            --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":
                    --readExtension3 $extended_parameters.read_extension_3p
                #end if

                $pe_parameters.fragment_counting_enabled.fragment_counting
                #if str($pe_parameters.fragment_counting_enabled.fragment_counting) == " -p":
                    $pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance
                    #if str($pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance) == " -P":
                        -d $pe_parameters.fragment_counting_enabled.check_distance_enabled.minimum_fragment_length
                        -D $pe_parameters.fragment_counting_enabled.check_distance_enabled.maximum_fragment_length
                    #end if
                #end if

                $pe_parameters.only_both_ends
                $pe_parameters.exclude_chimerics

        '${alignment}'

        ## Removal of comment
        && grep -v "^#" "output"

        #if $format.value != "tabdel_short":
            ## and remove column-header line
            | tail -n+2
        #else
            ## update header
            | sed --expression='s|${alignment}|${alignment.element_identifier}|g'
        #end if
        > body.txt
        ## Set the right columns for the tabular formats
        #if $format.value == "tabdel_medium":
            && cut -f 1,7 body.txt > expression_matrix.txt

            ## Paste doesn't allow a non ordered list of columns: -f 1,7,8,6 will only return columns 1,7 and 8
            ## Thus the gene length column (last column) has to be added separately
            && cut -f 6 body.txt > gene_lengths.txt
            && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak
            && mv -f expression_matrix.txt.bak '${output_medium}'
        #elif $format.value == "tabdel_short" or $format.value == "tabdel_short_noheader":
            && cut -f 1,7 body.txt > '${output_short}'
        #else:
            && cp body.txt '${output_full}'
        #end if

        #if str($include_feature_length_file) == "true":
            && cut -f 1,6 body.txt > '${output_feature_lengths}'
        #end if

        #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
            #if $format.value != "tabdel_short":
              && tail -n+2 'output.jcounts' > '${output_jcounts}'
            #else:

              && sed --expression='s|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}'
            #end if
        #end if

        #if $format.value != "tabdel_short":
            && tail -n+2 'output.summary' > '${output_summary}'
        #else:
            && sed --expression='s|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
        #end if
    ]]></command>
    <inputs>
        <param name="alignment"
               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" />
        <conditional name="anno">
            <param name="anno_select" type="select" label="Gene annotation file">
                <option value="builtin">featureCounts built-in</option>
                <option value="gtf">GTF file</option>
            </param>
            <when value="builtin">
                <param name="genome" type="select" label="Select built-in genome" help="Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts">
                    <option value="hg38">hg38</option>
                    <option value="hg19">hg19</option>
                    <option value="mm10">mm10</option>
                    <option value="mm9">mm9</option>
                </param>
            </when>
            <when value="gtf">
                <conditional name="gtf_source">
                    <param name="ref_source" type="select" label="Gene annotation file">
                        <option value="cached">locally cached</option>
                        <option value="history">in your history</option>
                    </param>
                    <when value="cached">
                        <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator">
                            <options from_data_table="gene_sets">
                                <filter type="sort_by" column="1" />
                                <validator type="no_options" message="No annotations are available." />
                            </options>
                        </param>
                    </when>
                    <when value="history">
                        <param name="reference_gene_sets"
                               format="gff,gtf,gff3"
                               type="data"
                               label="Gene annotation file"
                               help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment" />
                    </when>
                </conditional>
            </when>
        </conditional>

        <param name="format"
               type="select"
               label="Output format"
               help="The output format will be tabular, select the preferred columns here">
            <option value="tabdel_short_noheader" selected="true">Gene-ID "\t" read-count (DESeq2 IUC wrapper compatible)</option>
            <option value="tabdel_short">Gene-ID "\t" read-count (MultiQC/edgeR/limma-voom compatible, includes header in output)</option>
            <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option>
            <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option>
        </param>

        <param name="include_feature_length_file"

            <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue=""
                   label="Long reads"
                   help="If specified, long reads such as Nanopore and PacBio reads will be counted. Long read counting can only run in one thread and only reads (not read-pairs) can be counted." />

            <param name="by_read_group" argument="--byReadGroup" type="boolean" truevalue="--byReadGroup" falsevalue=""
                  label="Count reads by read group"
                  help="If specified, reads are counted for each read group separately. The 'RG' tag must be present in the input BAM/SAM alignment files." />


            <param name="largest_overlap"

                   value="1"
                   argument="--minOverlap"
                   label="Minimum bases of overlap"
                   help="Specify the minimum required number of overlapping bases between a read (or a fragment) and a feature. 1 by default. If a negative value is provided, the read will be extended from both ends." />

            <param name="frac_overlap"
                  type="integer"
                  value="0"
                  min="0"
                  max="1"
                  argument="--fracOverlap"
                  label="Minimum fraction (of read) overlapping a feature"
                  help="Specify the minimum required fraction of overlapping bases between a read (or a fragment) and a feature. Value should be within range [0,1]. 0 by default. Number of overlapping bases is counted from both reads if paired end. Both this option and '--minOverlap' need to be satisfied for read assignment." />

            <param name="frac_overlap_feature"
                     type="integer"
                     value="0"
                     min="0"
                     max="1"
                     argument="--fracOverlapFeature"

        </data>

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

            </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 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">
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="anno_select" value="gtf"/>
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <param name="format" value="tabdel_short_noheader" />
            <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"/>

                <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="anno_select" value="gtf"/>
            <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_1_medium.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="anno_select" value="gtf"/>
            <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_1_full.tab">

            </output>
            <output name="output_feature_lengths" file="output_feature_lengths.tab">
                <metadata name="column_names" value="Feature,Length"/>
            </output>
        </test>
        <test expect_num_outputs="4">
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
            <param name="anno_select" value="gtf"/>
            <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_with_header.tab">
                <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
            </output>
            <output name="output_summary" file="output_1_summary_with_header.tab">
                <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
            </output>
            <output name="output_jcounts" file="output_1_jcounts_with_header.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 built-in annotation works -->
        <test expect_num_outputs="2">
            <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" />
            <param name="anno_select" value="builtin"/>
            <param name="format" value="tabdel_short" />
            <param name="genome" value="hg19" />
            <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>
    </tests>

    <help><![CDATA[
featureCounts
#############

Overview
--------
FeatureCounts is a light-weight read counting program written entirely in the C programming language. It can be used to count both gDNA-seq and RNA-seq reads for genomic features in in SAM/BAM files. FeatureCounts is part of the Subread_ package.

Input formats
-------------
Alignments should be provided in either:

 - SAM format, http://samtools.sourceforge.net/samtools.shtml#5
 - BAM format

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 Galaxy wrapper by IUC. Column names are added as metadata object.

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