# HG changeset patch
# User iuc
# Date 1638656245 0
# Node ID 83ab9e468b869dbf314150144c81adf9387ac81d
# Parent  56aa64c236905831cd1e97c8428069d8a3b64d5d
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 839f962c859728f53bb696cea0720862418f1a13"

diff -r 56aa64c23690 -r 83ab9e468b86 featurecounts.xml
--- a/featurecounts.xml	Tue Aug 31 08:07:43 2021 +0000
+++ b/featurecounts.xml	Sat Dec 04 22:17:25 2021 +0000
@@ -2,7 +2,7 @@
     <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>
+        <token name="@VERSION_SUFFIX@">2</token>
     </macros>
     <xrefs>
         <xref type="bio.tools">subread</xref>
@@ -38,6 +38,12 @@
             -T \${GALAXY_SLOTS:-2}
 
             -s  $strand_specificity
+
+            -Q  $read_filtering_parameters.mapping_quality
+            $read_filtering_parameters.splitonly
+            $read_filtering_parameters.primary
+            $read_filtering_parameters.ignore_dup
+
             -t '$extended_parameters.gff_feature_type'
             -g '$extended_parameters.gff_feature_attribute'
                 $extended_parameters.summarization_level
@@ -66,14 +72,11 @@
 
                 $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
@@ -258,6 +261,33 @@
                 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="read_filtering_parameters" title="Read filtering options">
+            <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." />
+            <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">
             <param name="gff_feature_type"
                 type="text"
@@ -283,8 +313,8 @@
 
             <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>
@@ -295,8 +325,8 @@
                             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."/>
+                            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 name="fraction"
@@ -304,8 +334,8 @@
                             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."/>
+                            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 name="fraction"
@@ -313,18 +343,11 @@
                             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."/>
+                            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>
 
-            <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"
@@ -403,22 +426,6 @@
                 <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=""
@@ -426,13 +433,6 @@
                    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>
@@ -620,7 +620,7 @@
 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 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>
diff -r 56aa64c23690 -r 83ab9e468b86 featurecounts.xml.orig
--- a/featurecounts.xml.orig	Tue Aug 31 08:07:43 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,635 +0,0 @@
-<<<<<<< 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>