# HG changeset patch
# User iuc
# Date 1597393735 14400
# Node ID 90d16db017d7f81eba23ea479a273ae3927de921
# Parent  a37612abf7f92f09ace0ff1b14f164c60c76a538
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit d80704d28a7be0c42d41e48f8e12b9d727233be4"

diff -r a37612abf7f9 -r 90d16db017d7 featurecounts.xml
--- a/featurecounts.xml	Fri Sep 06 11:08:21 2019 -0400
+++ b/featurecounts.xml	Fri Aug 14 04:28:55 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="featurecounts" name="featureCounts" version="1.6.4+galaxy1" profile="16.04">
+<tool id="featurecounts" name="featureCounts" version="1.6.4+galaxy2" profile="16.04">
     <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
     <requirements>
         <requirement type="package" version="1.6.4">subread</requirement>
@@ -34,12 +34,19 @@
             -t '$extended_parameters.gff_feature_type'
             -g '$extended_parameters.gff_feature_attribute'
                 $extended_parameters.summarization_level
-                $extended_parameters.contribute_to_multiple_features
-                $extended_parameters.multimapping_enabled.multimapping_counts
+
+                $extended_parameters.multifeatures.multifeat
+                #if $extended_parameters.multifeatures.multifeat != "":
+                    $extended_parameters.multifeatures.fraction
+                #end if
+
 
-                #if str($extended_parameters.multimapping_enabled.multimapping_counts) == " -M":
-                    $extended_parameters.multimapping_enabled.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":
@@ -267,33 +274,41 @@
                 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)" />
-
-            <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>
+            <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=" -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 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="" />
+                <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"