diff featurecounts.xml @ 31:6f66ae7c5f7a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit a0d90afa3160e737786cc448aaf7c92df94a64cc

--- a/featurecounts.xml	Fri Feb 24 14:02:04 2023 +0000
+++ b/featurecounts.xml	Thu Mar 02 12:50:54 2023 +0000
@@ -2,7 +2,7 @@
     <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description>
     <macros>
         <token name="@TOOL_VERSION@">2.0.3</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
 
         <macro name="conditional_gff_opions">
             <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."/>
@@ -91,7 +91,7 @@
                     $pe_parameters.exclude_chimerics
                     #if str($pe_parameters.paired_end_status) == "PE_fragments":
                         --countReadPairs
-                        #if $pe_parameters.check_distance_enabled.checkFragLength:
+                        #if $pe_parameters.check_distance_enabled.checkFragLength == "true":
                             --checkFragLength
                             --minFragLength $pe_parameters.check_distance_enabled.minimum_fragment_length
                             --maxFragLength $pe_parameters.check_distance_enabled.maximum_fragment_length
@@ -549,6 +549,23 @@
             <output name="output_summary" file="output_summary_builtin_hg19.tab"/>
             <output name="output_bam" file="output.bam" ftype="bam"/>
         </test>
+        <!-- Ensure fragment counting works -->
+        <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"/>
+            <conditional name="pe_parameters">
+                <param name="paired_end_status" value="PE_fragments"/>
+            </conditional>
+            <section name="extended_parameters">
+                <param name="R" value="true"/>
+            </section>
+            <output name="output_short" file="output_builtin_hg19_fragment.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_fragments.tab"/>
+            <output name="output_bam" file="output_fragments.bam" ftype="bam"/>
+        </test>
         <!-- Ensure cached GTFs work -->
         <test expect_num_outputs="3">
             <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/>