diff varscan_somatic.xml @ 5:d37adcc2ec03 draft

planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 3a2e62daa15beefe2015ed68cc862b88ade31934

--- a/varscan_somatic.xml	Tue Dec 04 05:53:45 2018 -0500
+++ b/varscan_somatic.xml	Wed Dec 05 11:16:52 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.1">
+<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.2">
     <description>Call germline/somatic and LOH variants from tumor-normal sample pairs</description>
     <macros>
         <import>macros.xml</import>
@@ -38,13 +38,13 @@
     </stdio>
     <command><![CDATA[
         #if str($reference.source) == "history":
-            #set ref_genome = 'ref.fa'
+            #set $ref_genome = 'ref.fa'
             ln -s -f '$reference.genome' $ref_genome &&
         #else:
-            #set ref_genome = '$reference.genome.fields.path'
+            #set $ref_genome = str($reference.genome.fields.path)
         #end if
-        #set normal_data = 'normal.bam'
-        #set tumor_data = 'tumor.bam'
+        #set $normal_data = 'normal.bam'
+        #set $tumor_data = 'tumor.bam'
         ln -s -f '$normal_bam' $normal_data &&
         ln -s -f '$tumor_bam' $tumor_data &&
         ln -s -f '${normal_bam.metadata.bam_index}' ${normal_data}.bai &&
@@ -127,7 +127,7 @@
                 --max-mmqs-diff ${filter_params.max_mmqs_diff}
             #end if
             --verbose
-            $ref_genome
+            '$ref_genome'
     ]]></command>
 
     <inputs>
@@ -304,6 +304,25 @@
                 <expand macro="test_mentions_filters" />
             </output>
         </test>
+        <test expect_num_outputs="1">
+            <conditional name="reference">
+                <param name="source" value="cached" />
+                <param name="genome" value="hg19mito" />
+            </conditional>
+            <param name="normal_bam" dbkey="hg19" value="control_chrM.bam" />
+            <param name="tumor_bam" dbkey="hg19" value="tumor_chrM.bam" />
+            <param name="split_output" value="false" />
+            <conditional name="call_params">
+                <param name="settings" value="varscan_defaults" />
+            </conditional>
+            <conditional name="filter_params">
+                <param name="settings" value="varscan_defaults" />
+            </conditional>
+            <output name="output">
+                <expand macro="test_mentions_contig" />
+                <expand macro="test_mentions_filters" />
+            </output>
+        </test>
         <test expect_num_outputs="2">
             <conditional name="reference">
                 <param name="source" value="history" />