diff varscan_copynumber.xml @ 1:8d8de66233ea draft

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

--- a/varscan_copynumber.xml	Tue Jul 10 13:36:24 2018 -0400
+++ b/varscan_copynumber.xml	Sun Jul 15 09:19:48 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="varscan_copynumber" name="VarScan copynumber" version="@VERSION@.0">
+<tool id="varscan_copynumber" name="VarScan copynumber" version="@VERSION@.1">
     <description>Determine relative tumor copy number from tumor-normal pileups</description>
     <macros>
         <import>macros.xml</import>
@@ -8,9 +8,7 @@
     <command><![CDATA[
 
         varscan copynumber
-            '${normal_pileup}'
-            '${tumor_pileup}'
-            galaxy_out
+            @INPUT_PILEUPS@
             --min-coverage ${min_coverage}
             --min-base-qual ${min_base_qual}
             --min-map-qual ${min_map_qual}
@@ -23,8 +21,7 @@
     ]]></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"/>
 
         <param argument="--min-coverage" name="min_coverage" type="integer" value="20" min="1" max="200"
             label="Minimum read depth" help="Minimum coverage threshold for copynumber segments"/>
@@ -52,10 +49,20 @@
     </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>
             <output name="output" file="varscan_copynumber_result1.interval" lines_diff="0" />
         </test>
+        <test>
+            <conditional name="pileup">
+                <param name="pileup_select" value="combined" />
+                <param name="combined_pileup" value="NT.pileup.gz" />
+            </conditional>
+            <output name="output" file="varscan_copynumber_result2.interval" lines_diff="0" />
+        </test>
     </tests>
 
     <help>