diff featurecounts.xml @ 28:7db9d3ea71c9 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6ad844a722ddf6a71cae4c77bc43d3051376d891"

--- a/featurecounts.xml	Tue Jul 13 12:14:05 2021 +0000
+++ b/featurecounts.xml	Mon Aug 30 13:47:52 2021 +0000
@@ -281,8 +281,8 @@
 
             <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 +293,8 @@
                             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"
@@ -302,8 +302,8 @@
                             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"
@@ -311,8 +311,8 @@
                             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 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>