diff rg_rnaStarSolo.xml @ 20:45795f582ae9 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151

--- a/rg_rnaStarSolo.xml	Wed Feb 14 09:04:09 2024 +0000
+++ b/rg_rnaStarSolo.xml	Tue Aug 27 14:11:53 2024 +0000
@@ -94,6 +94,11 @@
     --soloCBwhitelist None
     #end if
 
+    #if $solo.wasp_conditional.waspOutputMode == "wasp_mode":
+        --waspOutputMode SAMtag
+        --varVCFfile '$solo.wasp_conditional.varVCFfile'
+    #end if
+
     --soloStrand $solo.soloStrand
     --soloFeatures $solo.soloFeatures
     --soloUMIdedup $sc.umidedup.soloUMIdedup
@@ -355,6 +360,7 @@
                 <option value="GeneFull_Ex50pAS" >Full: Count all reads overlapping genes' exons and introns: prioritize 50% overlap with exons. Do not count reads with 100% exonic overlap in the antisense direction.</option>
                 <option value="Gene Velocyto">Velocyto: calculate spliced, unspliced, and ambiguous counts per cell per gene similar to the velocyto tool</option>
             </param>
+            <expand macro="wasp"/>
             <conditional name="filter" >
                 <param name="filter_type" type="select" label="Cell filtering type and parameters" >
                     <option value="cellranger2" selected="true" >Simple filtering of CellRanger v2</option>
@@ -515,6 +521,10 @@
                 <param name="soloStrand" value="Forward" />
                 <param name="soloFeatures" value="Gene" />
                 <param name="quantModeGene" value="true" />
+                <conditional name="wasp_conditional">
+                    <param name="waspOutputMode" value="wasp_mode"/>
+                    <param name="varVCFfile" value="filtered3.vcf" ftype="vcf" />
+                </conditional>
             </section>
             <output name="output_barcodes" >
                 <assert_contents>
@@ -544,7 +554,7 @@
                     <has_line_matching expression="\s+yesUMIs\s+8" />
                 </assert_contents>
             </output>
-            <output name="output_BAM" value="filtered3.bam" compare="sim_size" delta="600" />
+            <output name="output_BAM" value="filtered4.bam" ftype="bam" lines_diff="6"/>
             <output name="reads_per_gene" >
                 <assert_contents>
                     <has_line_matching expression="ENSG00000279493\s+0\s+0\s+0" />