diff featurecounts.xml @ 17:8ce1e2c7ee72 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018

--- a/featurecounts.xml	Thu Jun 14 04:33:21 2018 -0400
+++ b/featurecounts.xml	Wed Jun 20 05:32:55 2018 -0400
@@ -1,7 +1,8 @@
-<tool id="featurecounts" name="featureCounts" version="1.6.0.6" profile="16.04">
+<tool id="featurecounts" name="featureCounts" version="1.6.0.7" profile="16.04">
     <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
     <requirements>
         <requirement type="package" version="1.6.0">subread</requirement>
+        <requirement type="package" version="1.7">samtools</requirement>
     </requirements>
 
     <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
@@ -58,7 +59,9 @@
                 $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 $extended_parameters.read_extension_5p
                 #end if
@@ -108,6 +111,9 @@
             && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}'
         #end if
 
+        #if $extended_parameters.R:
+            && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} *.featureCounts.bam
+        #end if
         && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
     ]]></command>
     <inputs>
@@ -389,6 +395,13 @@
                    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"
@@ -408,6 +421,12 @@
             </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}">
@@ -500,14 +519,18 @@
             </output>
         </test>
         <!-- Ensure featureCounts built-in annotation works -->
-        <test expect_num_outputs="2">
+        <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">