changeset 8:2a8bb8223a45 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 2228563ac1c2bb236c8ac83d08d2b86e21a39e41

--- a/featurecounts.xml	Mon Oct 30 14:49:13 2017 -0400
+++ b/featurecounts.xml	Wed Nov 15 15:53:25 2017 -0500
@@ -1,7 +1,7 @@
-<tool id="featurecounts" name="featureCounts" version="1.5.3" profile="16.04">
+<tool id="featurecounts" name="featureCounts" version="1.6.0" profile="16.04">
     <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
     <requirements>
-        <requirement type="package" version="1.5.3">subread</requirement>
+        <requirement type="package" version="1.6.0">subread</requirement>
     </requirements>
 
     <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
@@ -37,9 +37,13 @@
 
                 $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
                 $extended_parameters.ignore_dup
@@ -83,7 +87,7 @@
         #else
             && cp body.txt '${output_full}'
         #end if
-        
+
 
         #if str($include_feature_length_file) == "true"
             && cut -f 1,6 body.txt > '${output_feature_lengths}'
@@ -103,7 +107,7 @@
                format="bam,sam"
                label="Alignment file"
                help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format" />
-        
+
         <conditional name="gtf_source">
             <param name="ref_source" type="select" label="Gene annotation file">
                 <option value="cached">locally cached</option>
@@ -125,7 +129,7 @@
                        help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment" />
             </when>
         </conditional>
-        
+
         <param name="format"
                type="select"
                label="Output format"
@@ -134,7 +138,7 @@
             <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"
@@ -183,7 +187,7 @@
                 </when>
                 <when value="" />
             </conditional>
-            
+
             <param name="only_both_ends"
                    type="boolean"
                    truevalue=" -B"
@@ -201,7 +205,7 @@
                 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"
@@ -287,6 +291,11 @@
                    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"
@@ -299,9 +308,27 @@
                    type="integer"
                    value="1"
                    argument="--minOverlap"
-                   label="Minimum overlap"
+                   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"
@@ -325,7 +352,7 @@
                 <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"
@@ -333,7 +360,7 @@
                    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"
@@ -341,7 +368,7 @@
                    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 name="count_split_alignments_only"
                    type="boolean"
                    truevalue=" --countSplitAlignmentsOnly"
@@ -452,9 +479,9 @@
                 <metadata name="column_names" value="Feature,Length"/>
             </output>
         </test>
-        
+
     </tests>
-    
+
     <help><![CDATA[
 featureCounts
 #############