diff varscan_somatic.xml @ 1:31a38ce7e8ae draft

planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 33c5694cb2e0a86a76d12a3355a2bd26deba7177

--- a/varscan_somatic.xml	Tue Jul 10 13:35:40 2018 -0400
+++ b/varscan_somatic.xml	Sun Jul 15 09:19:25 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.0">
+<tool id="varscan_somatic" name="VarScan somatic" version="@VERSION@.1">
     <description>Call germline/somatic variants from tumor-normal pileups</description>
     <macros>
         <import>macros.xml</import>
@@ -7,9 +7,7 @@
     <expand macro="stdio" />
     <command><![CDATA[
         varscan somatic
-            '${normal_pileup}'
-            '${tumor_pileup}'
-            galaxy_out
+            @INPUT_PILEUPS@
             --min-coverage ${min_coverage}
             --min-reads2 ${min_reads2}
             --min-avg-qual ${min_avg_qual}
@@ -29,8 +27,8 @@
     ]]></command>
 
     <inputs>
-        <param name="normal_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
-        <param name="tumor_pileup" format="pileup" type="data" label="Samtools pileup dataset" help=""/>
+
+        <expand macro="input_pileups"/>
 
         <expand macro="min_coverage" />
         <param argument="--min-coverage-normal" name="min_coverage_normal" type="integer" value="8" min="1" max="200"
@@ -56,8 +54,11 @@
     </outputs>
     <tests>
         <test>
-            <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" />
-            <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" />
+            <conditional name="pileup">
+                <param name="pileup_select" value="separated" />
+                <param name="normal_pileup" value="N_Region_Chr1_CDKN2C.pileup.gz" />
+                <param name="tumor_pileup" value="T_Region_Chr1_CDKN2C.pileup.gz" />
+            </conditional>
             <param name="min_coverage" value="2" />
             <param name="min_coverage_normal" value="2" />
             <param name="min_coverage_tumor" value="2" />
@@ -71,6 +72,24 @@
             <output name="output_indel" file="varscan_somatic_indel_result1.vcf" lines_diff="0" />
             <output name="output_snp" file="varscan_somatic_snp_result1.vcf" lines_diff="0" />
         </test>
+        <test>
+            <conditional name="pileup">
+                <param name="pileup_select" value="combined" />
+                <param name="combined_pileup" value="NT.pileup.gz" />
+            </conditional>
+            <param name="min_coverage" value="2" />
+            <param name="min_coverage_normal" value="2" />
+            <param name="min_coverage_tumor" value="2" />
+            <param name="min_reads2" value="1" />
+            <param name="min_avg_qual" value="5" />
+            <param name="min_var_freq" value="0.01" />
+            <param name="min_freq_for_hom" value="0.75" />
+            <param name="normal_purity" value="0.6" />
+            <param name="tumor_purity" value="0.6" />
+            <param name="p_value" value="0.99" />
+            <output name="output_indel" file="varscan_somatic_indel_result2.vcf" lines_diff="0" />
+            <output name="output_snp" file="varscan_somatic_snp_result2.vcf" lines_diff="0" />
+        </test>
     </tests>
 
     <help>