# HG changeset patch
# User iuc
# Date 1630397263 0
# Node ID 56aa64c236905831cd1e97c8428069d8a3b64d5d
# Parent  3cd88f5c9d4ca0de8a7a7458cd9b42ab3d5f9cc2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

diff -r 3cd88f5c9d4c -r 56aa64c23690 featurecounts.xml
--- a/featurecounts.xml	Mon Aug 30 13:47:16 2021 +0000
+++ b/featurecounts.xml	Tue Aug 31 08:07:43 2021 +0000
@@ -1,10 +1,12 @@
 <tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
-    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
+    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description>
     <macros>
         <token name="@TOOL_VERSION@">2.0.1</token>
         <token name="@VERSION_SUFFIX@">1</token>
     </macros>
-
+    <xrefs>
+        <xref type="bio.tools">subread</xref>
+    </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">subread</requirement>
         <requirement type="package" version="1.11">samtools</requirement>
@@ -281,8 +283,8 @@
 
             <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="" 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>
@@ -293,8 +295,8 @@
                             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."/>
+                            label="Assign fractions to multimapping reads"
+                            help="If specified, a fractional count 1/n will be generated for each multi-mapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/>
                 </when>
                 <when value="-O">
                         <param name="fraction"
@@ -302,8 +304,8 @@
                             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."/>
+                            label="Assign fractions to multimapping reads"
+                            help="If specified, a fractional count 1/n will be generated for each multi-overlapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/>
                 </when>
                 <when value="-O -M">
                         <param name="fraction"
@@ -311,8 +313,8 @@
                             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."/>
+                            label="Assign fractions to multimapping reads"
+                            help="If specified, a fractional count 1/n will be generated for each multi-mapping or multi-overlapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/>
                 </when>
             </conditional>
 
diff -r 3cd88f5c9d4c -r 56aa64c23690 featurecounts.xml.orig
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/featurecounts.xml.orig	Tue Aug 31 08:07:43 2021 +0000
@@ -0,0 +1,635 @@
+<<<<<<< HEAD
+<tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
+    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.0.1</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+    </macros>
+
+=======
+<tool id="featurecounts" name="featureCounts" version="2.0.1" profile="16.04">
+    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description>
+    <xrefs>
+        <xref type='bio.tools'>subread</xref>
+    </xrefs>
+>>>>>>> d0c3b656f (add bio.tools ID)
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">subread</requirement>
+        <requirement type="package" version="1.11">samtools</requirement>
+        <requirement type="package" version="8.31">coreutils</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_builtin.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  $strand_specificity
+            -t '$extended_parameters.gff_feature_type'
+            -g '$extended_parameters.gff_feature_attribute'
+                $extended_parameters.summarization_level
+
+                $extended_parameters.multifeatures.multifeat
+                #if $extended_parameters.multifeatures.multifeat != "":
+                    $extended_parameters.multifeatures.fraction
+                #end if
+
+
+                ## $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 -->
+
+                $extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads
+                #if str($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
+
+            -Q  $extended_parameters.mapping_quality
+                $extended_parameters.largest_overlap
+            --minOverlap  $extended_parameters.min_overlap
+            --fracOverlap $extended_parameters.frac_overlap
+            --fracOverlapFeature $extended_parameters.frac_overlap_feature
+                $extended_parameters.read_reduction
+                $extended_parameters.primary
+                $extended_parameters.ignore_dup
+                #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
+
+                $pe_parameters.fragment_counting_enabled.fragment_counting
+                #if str($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}'
+
+        ## 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">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"/>
+                    </options>
+                </param>
+            </when>
+            <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="data_meta" key="dbkey" ref="alignment" column="dbkey"/>
+                        <filter type="sort_by" column="2" />
+                    </options>
+                    <validator type="no_options" message="An annotation file is not available for the build associated with the selected input file"/>
+                </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">
+                </param>
+            </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" />
+
+
+        <section name="pe_parameters" title="Options for paired-end reads">
+            <conditional name="fragment_counting_enabled">
+
+                <param name="fragment_counting"
+                       type="select"
+                       argument="-p"
+                       checked="true"
+                       label="Count fragments instead of reads"
+                       help="If specified, fragments (or templates) will be counted instead of reads.">
+                    <option value="" selected="true">Disabled; all reads/mates will be counted individually</option>
+                    <option value=" -p">Enabled; fragments (or templates) will be counted instead of reads</option>
+                </param>
+
+                <when value=" -p">
+                    <conditional name="check_distance_enabled">
+                        <param name="check_distance"
+                            type="boolean"
+                            truevalue=" -P"
+                            falsevalue=""
+                            argument="-P"
+                            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 should be specified using -d and -D (minimum and maximum fragment/template length) options." />
+                        <when value=" -P">
+                            <param name="minimum_fragment_length"
+                                   type="integer"
+                                   value="50"
+                                   argument="-d"
+                                   label="Minimum fragment/template length." />
+                            <param name="maximum_fragment_length"
+                                   type="integer"
+                                   value="600"
+                                   argument="-D"
+                                   label="Maximum fragment/template length." />
+                        </when>
+                        <when value="" />
+                    </conditional>
+                </when>
+                <when value="" />
+            </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." />
+        </section>
+
+        <section name="extended_parameters" title="Advanced options">
+            <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." />
+
+            <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." />
+
+            <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 name="fraction"
+                            type="boolean"
+                            truevalue="--fraction"
+                            falsevalue=""
+                            argument="--fraction"
+                            label="Assign fractions to multimapping reads"
+                            help="If specified, a fractional count 1/n will be generated for each multi-mapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/>
+                </when>
+                <when value="-O">
+                        <param name="fraction"
+                            type="boolean"
+                            truevalue="--fraction"
+                            falsevalue=""
+                            argument="--fraction"
+                            label="Assign fractions to multimapping reads"
+                            help="If specified, a fractional count 1/n will be generated for each multi-overlapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/>
+                </when>
+                <when value="-O -M">
+                        <param name="fraction"
+                            type="boolean"
+                            truevalue="--fraction"
+                            falsevalue=""
+                            argument="--fraction"
+                            label="Assign fractions to multimapping reads"
+                            help="If specified, a fractional count 1/n will be generated for each multi-mapping or multi-overlapping read, where n is the number of alignments (indica- ted by 'NH' tag) reported for the read."/>
+                </when>
+            </conditional>
+
+            <param name="mapping_quality"
+                   type="integer"
+                   value="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." />
+
+            <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>
+
+            <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"
+                   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"
+                   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 name="primary"
+                   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." />
+
+            <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="" />
+
+            <param name="count_split_alignments_only"
+                   type="boolean"
+                   truevalue=" --countSplitAlignmentsOnly"
+                   falsevalue=""
+                   argument="--countSplitAlignmentsOnly"
+                   label="Ignore unspliced alignments"
+                   help="If specified, only split alignments (CIGAR strings containing the letter `N') will be counted. All the other alignments will be ignored. An example of split alignments are exon-spanning reads in RNA-seq data." />
+        </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" />
+            <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 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  -
+  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. 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`: 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>