--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/featurecounts.xml	Wed Sep 21 07:24:39 2016 -0400
@@ -0,0 +1,442 @@
+<tool id="featurecounts" name="featureCounts" version="1.4.6.p5" profile="16.04">
+    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
+    <requirements>
+        <requirement type="package" version="1.4.6p5">subread</requirement>
+    </requirements>
+
+    <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
+    <command><![CDATA[
+        ## Check whether all alignments are from the same type (bam || sam)
+        featureCounts
+            -a "$reference_gene_sets"
+            -o "output"
+            -T \${GALAXY_SLOTS:-2}
+
+            -t "$extended_parameters.gff_feature_type"
+            -g "$extended_parameters.gff_feature_attribute"
+                $extended_parameters.summarization_level
+                $extended_parameters.contribute_to_multiple_features
+            -s  $extended_parameters.strand_specificity
+                $extended_parameters.multimapping_enabled.multimapping_counts
+
+                #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M"
+                    $extended_parameters.multimapping_enabled.fraction
+                #end if
+
+            -Q  $extended_parameters.mapping_quality
+                $extended_parameters.largest_overlap
+  --minOverlap  $extended_parameters.min_overlap
+                $extended_parameters.read_reduction
+                $extended_parameters.primary
+                $extended_parameters.ignore_dup
+
+                #if str($extended_parameters.read_extension_5p) != "0"
+                    --readExtension5 $extended_parameters.read_extension_5p
+                #end if
+
+                #if str($extended_parameters.read_extension_3p) != "0"
+                    --readExtension3 $extended_parameters.read_extension_3p
+                #end if
+
+                $pe_parameters.fragment_counting_enabled.fragment_counting
+                #if str($pe_parameters.fragment_counting_enabled.fragment_counting) == " -p"
+                    $pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance
+                    #if str($pe_parameters.fragment_counting_enabled.check_distance_enabled.check_distance) == " -P"
+                        -d $pe_parameters.fragment_counting_enabled.check_distance_enabled.minimum_fragment_length
+                        -D $pe_parameters.fragment_counting_enabled.check_distance_enabled.maximum_fragment_length
+                    #end if
+                #end if
+
+                $pe_parameters.only_both_ends
+            -S  $pe_parameters.orientation
+                $pe_parameters.exclude_chimerics
+
+        "${alignment}"
+
+        ## Removal of comment and column-header line
+        && grep -v "^#" "output" | tail -n+2 > body.txt
+
+        ## Set the right columns for the tabular formats
+        #if $format.value == "tabdel_medium"
+            && cut -f 1,7 body.txt > expression_matrix.txt
+
+            ## Paste doesn't allow a non ordered list of columns: -f 1,7,8,6 will only return columns 1,7 and 8
+            ## Thus the gene length column (last column) has to be added separately
+            && cut -f 6 body.txt > gene_lengths.txt
+            && paste expression_matrix.txt gene_lengths.txt > expression_matrix.txt.bak
+            && mv -f expression_matrix.txt.bak "${output_medium}"
+        #elif $format.value == "tabdel_short"
+            && cut -f 1,7 body.txt > "${output_short}"
+        #else
+            && cp body.txt "${output_full}"
+        #end if
+        
+
+        #if str($include_feature_length_file) == "true"
+            && cut -f 1,6 body.txt > "${output_feature_lengths}"
+        #end if
+
+        && tail -n+2 "output.summary" > "${output_summary}"
+
+    ]]></command>
+    <inputs>
+        <param name="alignment"
+               type="data"
+               multiple="false"
+               format="bam,sam"
+               label="Alignment file"
+               help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format" />
+        
+        <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 name="format"
+               type="select"
+               label="Output format"
+               help="The output format will be tabular, select the preferred columns here">
+            <option value="tabdel_short" selected="true">Gene-ID "\t" read-count (DESeq2 IUC wrapper compatible)</option>
+            <option value="tabdel_medium">Gene-ID "\t" read-count "\t" gene-length</option>
+            <option value="tabdel_full">featureCounts 1.4.0+ default (includes regions provided by the GTF file)</option>
+        </param>
+        
+        <param name="include_feature_length_file"
+               type="boolean"
+               truevalue="true"
+               falsevalue="false"
+               selected="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="orientation"
+                   type="select"
+                   label="Orientation of the two read from the same pair"
+                   argument="-S"
+                   help="Default is 'fr'">
+                <option value="fr" selected="true">Forward, Reverse (fr)</option>
+                <option value="ff">Forward, Forward (ff)</option>
+                <option value="rf">Reverse, Forward (rf)</option>
+            </param>
+
+            <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." />
+
+            <param name ="contribute_to_multiple_features"
+                type="boolean"
+                truevalue=" -O"
+                falsevalue=""
+                argument="-O"
+                label="Allow read to contribute to multiple features"
+                help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta- feature (or matched feature if -f is specified)" />
+
+            <param name="strand_specificity"
+                   type="select"
+                   label="Strand specificity of the protocol"
+                   argument="-s"
+                   help="Indicate if strand-specific read counting should be performed.">
+                <option value="0" selected="true">Unstranded</option>
+                <option value="1">Stranded (forwards)</option>
+                <option value="2">Stranded (reverse)</option>
+            </param>
+
+            <conditional name="multimapping_enabled">
+                <param name="multimapping_counts"
+                       type="select"
+                       argument="-M"
+                       label="Count multi-mapping reads/fragments"
+                       help="If specified, multi-mapping reads/fragments will be counted (ie. a multi-mapping read will be counted up to N times if it has N reported mapping locations). The program uses the `NH' tag to find multi-mapping reads.">
+                    <option value="" selected="true">Disabled; multi-mapping reads are excluded (default)</option>
+                    <option value=" -M">Enabled; multi-mapping reads are included</option>
+                </param>
+                <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. This option must be used together with the '-M' option." />
+                </when>
+                <when value="" />
+            </conditional>
+
+            <param name="mapping_quality"
+                   type="integer"
+                   value="12"
+                   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. 12 by default." />
+
+            <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 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="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 thesingle base which 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. Primaryand secondary alignments are identified using bit 0x100 in theFlag field of SAM/BAM files. All primary alignments in a datasetwill be counted no matter they are from multi-mapping reads ornot ('-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 asduplicates will be ignored. Bit Ox400 in FLAG field of SAM/BAMfile is used for identifying duplicate reads. In paired enddata, the entire read pair will be ignored if at least one endis found to be a duplicate read." />
+            
+            <param name="count_split_alignments_only"
+                   type="boolean"
+                   truevalue=" --countSplitAlignmentsOnly"
+                   falsevalue=""
+                   argument="--countSplitAlignmentsOnly"
+                   label="Ignore reads marked as duplicate"
+                   help="If specified, only split alignments (CIGARstrings containing letter `N') will be counted. All the otheralignments will be ignored. An example of split alignments isthe exon-spanning reads in RNA-seq data." />
+        </section>
+    </inputs>
+    <outputs>
+        <data format="tabular"
+              name="output_medium"
+              label="${tool.name} on ${on_string}">
+            <filter>format == "tabdel_medium"</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Geneid,${alignment.name},Length" />
+            </actions>
+        </data>
+
+        <data format="tabular"
+              name="output_short"
+              label="${tool.name} on ${on_string}">
+            <filter>format == "tabdel_short"</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Geneid,${alignment.name}" />
+            </actions>
+        </data>
+
+        <data format="tabular"
+              name="output_full"
+              label="${tool.name} on ${on_string}: count table">
+            <filter>format == "tabdel_full"</filter>
+            <actions>
+                <action name="column_names" type="metadata" default="Geneid,Chr,Start,End,Strand,Length,${alignment.name}" />
+            </actions>
+        </data>
+
+        <data format="tabular"
+              name="output_summary"
+              hidden="true"
+              label="${tool.name} on ${on_string}: summary">
+            <actions>
+                <action name="column_names" type="metadata" default="Status,${alignment.name}" />
+            </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>
+    </outputs>
+    <tests>
+        <test>
+            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
+            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
+            <param name="format" value="tabdel_short" />
+            <param name="include_feature_length_file" value="true"/>
+            <output name="output" file="output_1_short.tab"/>
+            <output name="output_summary" file="output_1_summary.tab"/>
+        </test>
+        <test>
+            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
+            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
+            <param name="format" value="tabdel_medium" />
+            <param name="include_feature_length_file" value="true"/>
+            <output name="output" file="output_1_medium.tab"/>
+            <output name="output_summary" file="output_1_summary.tab"/>
+        </test>
+        <test>
+            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
+            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
+            <param name="format" value="tabdel_full" />
+            <param name="include_feature_length_file" value="true"/>
+            <output name="output" file="output_1_full.tab"/>
+            <output name="output_summary" file="output_1_summary.tab"/>
+            <output name="output_feature_lengths" file="output_feature_lengths.tab"/>
+        </test>
+        
+        <test>
+            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
+            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
+            <param name="format" value="tabdel_short" />
+            <param name="include_feature_length_file" value="true"/>
+            <output name="output" file="output_2_short.tab"/>
+            <output name="output_summary" file="output_2_summary.tab"/>
+        </test>
+        <test>
+            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
+            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
+            <param name="format" value="tabdel_medium" />
+            <param name="include_feature_length_file" value="true"/>
+            <output name="output" file="output_2_medium.tab"/>
+            <output name="output_summary" file="output_2_summary.tab"/>
+        </test>
+        <test>
+            <param name="alignment" value="featureCounts_input1.bam" ftype="bam" />
+            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
+            <param name="format" value="tabdel_full" />
+            <param name="include_feature_length_file" value="true"/>
+            <output name="output" file="output_2_full.tab"/>
+            <output name="output_summary" file="output_2_summary.tab"/>
+            <output name="output_feature_lengths" file="output_feature_lengths.tab"/>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+featureCounts
+#############
+
+Overview
+--------
+FeatureCounts is a light-weight read counting program written entirely in the C programming language. It can be used to count both gDNA-seq and RNA-seq reads for genomic features in in SAM/BAM files.
+
+Input formats
+-------------
+Alignments should be provided in either:
+
+ - SAM format, http://samtools.sourceforge.net/samtools.shtml#5
+ - BAM format
+
+Gene regions should be provided in the GFF/GTF format:
+
+ - http://genome.ucsc.edu/FAQ/FAQformat.html#format3
+ - http://www.ensembl.org/info/website/upload/gff.html
+
+Output format
+-------------
+FeatureCounts produces a table containing the counted reads, per gene, per row. Optionally the last column can be set to be the effective gene-length. These tables are compatible with the DESeq2 Galaxy wrapper by IUC.
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btt656</citation>
+    </citations>
+</tool>