view featurecounts.xml @ 31:6f66ae7c5f7a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc
author iuc
date Thu, 02 Mar 2023 12:50:54 +0000
parents a56fbe2d6ba7
children f9d49f5cb597
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<tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description>
    <macros>
        <token name="@TOOL_VERSION@">2.0.3</token>
        <token name="@VERSION_SUFFIX@">1</token>

        <macro name="conditional_gff_opions">
            <param name="gff_feature_type" type="text" value="exon" argument="-t" label="GFF feature type filter" help="Specify the feature type. Only rows which have the matched matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default."/>
            <param name="gff_feature_attribute" type="text" value="gene_id" argument="-g" label="GFF gene identifier" help="Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes), when GTF annotation is provided. `gene_id' by default. This attribute type is usually the gene identifier. This argument is useful for the meta-feature level summarization. Ex: if the 9th column is 'gene_id &quot;ENSG00000223972&quot;; gene_name &quot;DDX11L1&quot; gene_source &quot;havana&quot;' (GTF) or 'gene_id=ENSG00000223972; gene_name=DDX11L1; gene_source=havana' (GFF), the available attributes for this feature are 'gene_id', 'gene_name' and 'gene_source'."/>
            <param name="summarization_level" type="boolean" truevalue=" -f" falsevalue="" argument="-f" label="On feature level" help="If specified, read summarization will be performed at the feature level. By default (-f is not specified), the read summarization is performed at the meta-feature level."/>
        </macro>
    </macros>
    <xrefs>
        <xref type="bio.tools">featurecounts</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">subread</requirement>
        <requirement type="package" version="1.16.1">samtools</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 $anno.anno_select=="history":
                -a '$anno.reference_gene_sets'
                -F "GTF"
            #elif $anno.anno_select=="cached":
                -a '$anno.reference_gene_sets_cached.fields.path'
                -F "GTF"
            #elif $anno.anno_select=="builtin":
                -a \${FC_PATH}/annotation/${anno.bgenome}_RefSeq_exon.txt
                -F "SAF"
            #end if

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

            -s  $strand_specificity

            -Q  $read_filtering_parameters.mapping_quality
            $read_filtering_parameters.splitonly
            $read_filtering_parameters.primary
            $read_filtering_parameters.ignore_dup

            #if $anno.anno_select!="builtin":
                -t '$anno.gff_feature_type'
                -g '$anno.gff_feature_attribute'
                    $anno.summarization_level
            #end if

                $extended_parameters.multifeatures.multifeat
                #if $extended_parameters.multifeatures.multifeat != "":
                    $extended_parameters.multifeatures.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

                $extended_parameters.by_read_group

                $extended_parameters.largest_overlap
            --minOverlap  $extended_parameters.min_overlap
            --fracOverlap $extended_parameters.frac_overlap
            --fracOverlapFeature $extended_parameters.frac_overlap_feature
                $extended_parameters.read_reduction
                #if $extended_parameters.R:
                    $extended_parameters.R
                #end if
                #if str($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
                
                #if str($pe_parameters.paired_end_status) != "single_end":
                    -p
                    $pe_parameters.only_both_ends
                    $pe_parameters.exclude_chimerics
                    #if str($pe_parameters.paired_end_status) == "PE_fragments":
                        --countReadPairs
                        #if $pe_parameters.check_distance_enabled.checkFragLength == "true":
                            --checkFragLength
                            --minFragLength $pe_parameters.check_distance_enabled.minimum_fragment_length
                            --maxFragLength $pe_parameters.check_distance_enabled.maximum_fragment_length
                        #end if
                    #end if
                #end if

        '${alignment}'

        ## Remove comment and add sample name to header
        && grep -v "^#" "output" 
        | sed -e 's|${alignment}|${alignment.element_identifier}|g'
        > 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($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
            && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}'
        #end if

        #if $extended_parameters.R:
            && samtools sort --no-PG -o '$output_bam' -@ \${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" *.featureCounts.bam
        #end if
        && sed -e 's|${alignment}|${alignment.element_identifier}|g' '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. 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>
                <option value="cached" selected="True">locally cached</option>
                <option value="history">A GFF/GTF file in your history</option>
            </param>
            <when value="builtin">
                <param name="bgenome" type="select" label="Select built-in genome" help="Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts">
                    <options from_data_table="featurecounts_anno">
                        <filter type="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
                        <filter type="sort_by" column="1"/>
                    </options>
                    <validator type="no_options" message="An built-in annotation file is not available for the genome build associated with the selected input file"/>
                </param>
            </when>
            <when value="cached">
                <param name="reference_gene_sets_cached" 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="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
                        <filter type="sort_by" column="2"/>
                    </options>
                    <validator type="no_options" message="A cached annotation file is not available for the genome build associated with the selected input file"/>
                </param>
                <expand macro="conditional_gff_opions"/>
            </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 GFF/GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment.">
                </param>
                <expand macro="conditional_gff_opions"/>
            </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">Gene-ID "\t" read-count (MultiQC/DESeq2/edgeR/limma-voom 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"
               type="boolean"
               truevalue="true"
               falsevalue="false"
               checked="false"
               label="Create gene-length file"
               help="Creates a tabular file that contains the effective (nucleotides used for counting reads) length of the feature; might be useful for estimating FPKM/RPKM"/>

        <conditional name="pe_parameters">
            <param name="paired_end_status" type="select" label="Does the input have read pairs?" help="Were the bam files generated by aligning the output of a paired-end sequencing experiment? If yes, the tool can consider 2 reads = 1 read pair as 1 entity to count. Alternatively, you can opt to consider treating the read pairs as 2 individual reads to count seperately.">
                <option value="single_end" selected="True">No, single-end.</option>
                <option value="PE_individual">Yes, paired-end but still count them as if individual reads.</option>
                <option value="PE_fragments">Yes, paired-end and count them as 1 single fragment.</option>
            </param>

            <when value="single_end"/>
            <when value="PE_individual">
                <param name="only_both_ends"
                    type="boolean"
                    truevalue=" -B"
                    falsevalue=""
                    argument="-B"
                    label="Only allow fragments with both reads aligned"
                    help="If specified, only fragments that have both ends successfully aligned will be considered for summarization. This option is only applicable for paired-end reads."/>

                <param name="exclude_chimerics"
                    type="boolean"
                    truevalue=" -C"
                    falsevalue=""
                    argument="-C"
                    checked="true"
                    label="Exclude chimeric fragments"
                    help="If specified, the chimeric fragments (those fragments that have their two ends aligned to different chromosomes) will NOT be included for summarization. This option is only applicable for paired-end read data."/>         
            </when>
            <when value="PE_fragments">
                <conditional name="check_distance_enabled">
                    <param argument="--checkFragLength" type="select" label="Check paired-end distance" help="If specified, paired-end distance will be checked when assigning fragments to meta-features or features. This option is only applicable when -p (Count fragments instead of reads) is specified. The distance thresholds can be specified using -d and -D (minimum and maximum fragment/template length) options.">
                        <option value="true">Check the distance between paired reads</option>
                        <option value="false" selected="True">Do not check</option>
                    </param>
                    <when value="true">
                        <param name="minimum_fragment_length"
                            type="integer"
                            value="50"
                            min="0"
                            argument="-d"
                            label="Minimum fragment/template length."/>
                        <param name="maximum_fragment_length"
                            type="integer"
                            value="600"
                            min="1"
                            argument="-D"
                            label="Maximum fragment/template length."/>
                    </when>
                    <when value="false"/>
                </conditional>
                
                <param name="only_both_ends"
                    type="boolean"
                    truevalue=" -B"
                    falsevalue=""
                    argument="-B"
                    label="Only allow fragments with both reads aligned"
                    help="If specified, only fragments that have both ends successfully aligned will be considered for summarization. This option is only applicable for paired-end reads."/>

                <param name="exclude_chimerics"
                    type="boolean"
                    truevalue=" -C"
                    falsevalue=""
                    argument="-C"
                    checked="true"
                    label="Exclude chimeric fragments"
                    help="If specified, the chimeric fragments (those fragments that have their two ends aligned to different chromosomes) will NOT be included for summarization. This option is only applicable for paired-end read data."/>      
            </when>
        </conditional>

        <section name="read_filtering_parameters" title="Read filtering options">
            <param name="mapping_quality"
                   type="integer"
                   value="0"
                   min="0"
                   argument="-Q"
                   label="Minimum mapping quality per read"
                   help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 0 by default."/>
            <param name="splitonly" type="select" display="radio" label="Filter split alignments" help="Split alignments are alignments with CIGAR string containing 'N', e.g. exon spanning reads in RNASeq.">
                <option value="">No filtering: count split and non-split alignments</option>
                <option value="--splitOnly">Count only split alignments (--splitOnly)</option>
                <option value="--nonSplitOnly">Count only non-split alignments (--nonSplitOnly)</option>
            </param>
            <param type="boolean"
                   truevalue=" --primary"
                   falsevalue=""
                   argument="--primary"
                   label="Only count primary alignments"
                   help="If specified, only primary alignments will be counted. Primary and secondary alignments are identified using bit 0x100 in theFlag field of SAM/BAM files. All primary alignments in a dataset will be counted regardless of whether they are from multi-mapping reads or not ('-M' is ignored)."/>
            <param name="ignore_dup"
                   type="boolean"
                   truevalue=" --ignoreDup"
                   falsevalue=""
                   argument="--ignoreDup"
                   label="Ignore reads marked as duplicate"
                   help="If specified, reads that were marked as duplicates will be ignored. Bit Ox400 in the FLAG field of a SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read."/>
        </section>

        <section name="extended_parameters" title="Advanced options">
            <conditional name = "multifeatures">
                <param name="multifeat" type="select" label="Allow reads to map to multiple features" help="Setting -O, -M and --fraction">
                    <option value="" selected="true">Disabled: reads that align to multiple features or overlapping features are excluded</option>
                    <option value="-M">Enabled: multi-mapping reads are included (-M)</option>
                    <option value="-O">Enabled: multi-overlapping features are included (-O)</option>
                    <option value="-O -M">Enabled: both multi-mapping and multi-overlapping features are included (-M -O)</option>
                </param>
                <when value=""/>
                <when value="-M">
                        <param type="boolean"
                            truevalue="--fraction"
                            falsevalue=""
                            argument="--fraction"
                            label="Assign fractions to multi-mapping reads"
                            help="If specified, a fractional count 1/x will be generated for each multi-mapping read, where x is the number of alignments (indicated by 'NH' tag) reported for the read."/>
                </when>
                <when value="-O">
                        <param type="boolean"
                            truevalue="--fraction"
                            falsevalue=""
                            argument="--fraction"
                            label="Assign fractions to multi-overlapping features"
                            help="If specified, a fractional count 1/y will be generated for each multi-overlapping feature, where y is the number of features overlapping with the read."/>
                </when>
                <when value="-O -M">
                        <param type="boolean"
                            truevalue="--fraction"
                            falsevalue=""
                            argument="--fraction"
                            label="Assign fractions to both multi-mapping reads and multi-overlapping features"
                            help="If specified, a fractional count 1/(x*y) will be generated, where x is the number of alignments (indicated by 'NH' tag) and y the number of overlapping features."/>
                </when>
            </conditional>

            <conditional name="exon_exon_junction_read_counting_enabled">
                <param name="count_exon_exon_junction_reads" type="select" argument="-J" label="Exon-exon junctions" help="Junctions are identified from those exon-spanning reads (containing ā€˜Nā€™ in CIGAR string) in input data. The output result includes names of primary and secondary genes that overlap at least one of the two splice sites of a junction.">
                    <option value="-J">Count reads supporting each exon-exon junction.</option>
                    <option value="" selected="True">Do not count</option>
                </param>
                <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>

            <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"
                   type="boolean"
                   truevalue=" --largestOverlap"
                   falsevalue=""
                   argument="--largestOverlap"
                   label="Largest overlap"
                   help="If specified, reads (or fragments) will be assigned to the target that has the largest number of overlapping bases"/>

            <param name="min_overlap"
                   type="integer"
                   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"
                     label="Minimum fraction (of feature) overlapping a read"
                     help="Specify the minimum required fraction of bases included in a feature overlapping bases between a read (or a read-pair). Value should be within range [0,1]. 0 by default."/>

            <param name="read_extension_5p"
                   type="integer"
                   value="0"
                   min="0"
                   argument="--readExtension5"
                   label="Read 5' extension"
                   help="Reads are extended upstream by ... bases from their 5' end"/>

            <param name="read_extension_3p"
                   type="integer"
                   value="0"
                   min="0"
                   argument="--readExtension3"
                   label="Read 3' extension"
                   help="Reads are extended upstream by ... bases from their 3' end"/>

            <param name="read_reduction"
                   type="select"
                   label="Reduce read to single position"
                   argument="--read2pos"
                   help="The read is reduced to its 5' most base or 3'most base. Read summarization is then performed based on the single base the the read is reduced to.">
                <option value="" selected="true">Leave the read as it is</option>
                <option value="--read2pos 5">Reduce it to the 5' end</option>
                <option value="--read2pos 3">Reduce it to the 3' end</option>
            </param>

            <param type="boolean"
                   truevalue="-R BAM"
                   falsevalue=""
                   argument="-R"
                   label="Annotates the alignment file with 'XS:Z:'-tags to described per read or read-pair the corresponding assigned feature(s)."
                   help=""/>

        </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>

        <data format="bam"
              name="output_bam"
              label="${tool.name} on ${on_string}: Alignment file">
            <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>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/>
            <param name="anno_select" value="history"/>
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
            <param name="format" value="tabdel_medium"/>
            <param name="include_feature_length_file" value="true"/>
            <output name="output_medium" file="output_1_medium.tab">
                <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
            </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" dbkey="hg38"/>
            <param name="anno_select" value="history"/>
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
            <param name="format" value="tabdel_full"/>
            <param name="include_feature_length_file" value="true"/>
            <output name="output_full" file="output_1_full.tab">
                <metadata name="column_names" value="Geneid,Chr,Start,End,Strand,Length,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_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" dbkey="hg38"/>
            <param name="anno_select" value="history"/>
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
            <param name="format" value="tabdel_short"/>
            <param name="include_feature_length_file" value="true"/>
            <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>
        <!-- Ensure featureCounts built-in annotation works -->
        <test expect_num_outputs="3">
            <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19"/>
            <param name="anno_select" value="builtin"/>
            <param name="format" value="tabdel_short"/>
            <conditional name="pe_parameters">
                <param name="paired_end_status" value="PE_individual"/>
            </conditional>
            <section name="extended_parameters">
                <param name="R" value="true"/>
            </section>
            <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"/>
            <output name="output_bam" file="output.bam" ftype="bam"/>
        </test>
        <!-- Ensure fragment counting works -->
        <test expect_num_outputs="3">
            <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19"/>
            <param name="anno_select" value="builtin"/>
            <param name="format" value="tabdel_short"/>
            <conditional name="pe_parameters">
                <param name="paired_end_status" value="PE_fragments"/>
            </conditional>
            <section name="extended_parameters">
                <param name="R" value="true"/>
            </section>
            <output name="output_short" file="output_builtin_hg19_fragment.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_fragments.tab"/>
            <output name="output_bam" file="output_fragments.bam" ftype="bam"/>
        </test>
        <!-- Ensure cached GTFs work -->
        <test expect_num_outputs="3">
            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/>
            <param name="anno_select" value="cached"/>
            <param name="format" value="tabdel_medium"/>
            <param name="include_feature_length_file" value="true"/>
            <output name="output_medium" file="output_1_medium.tab">
                <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
            </output>
            <output name="output_summary" file="output_1_summary.tab">
                <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
            </output>
        </test>
        <!-- Ensure BAM output works -->
        <test>
            <param name="alignment" value="subset.sorted.bam" ftype="bam"/>
            <param name="anno_select" value="history"/>
            <param name="reference_gene_sets" value="small.gtf" ftype="gtf"/>
            <section name="extended_parameters">
                <param name="R" value="true"/>
            </section>
            <output name="output_bam" value="subset.sorted.featurecounts.bam" compare="sim_size"/>
        </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 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  -
  497098  chr1  3411783  3411982  -
  497099  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. Gene names can be obtained for these Entrez identifiers with the Galaxy **annotateMyIDs** tool.

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`: https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf
.. _`Subread package`: https://sourceforge.net/projects/subread/files/
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btt656</citation>
    </citations>
</tool>