Mercurial > repos > matthias > stacks2_gstacks

diff stacks_gstacks.xml @ 1:192f1d5f301e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 8b047549e9e8791a5ca9424b1ef391e8980aba79-dirty
author matthias
date Fri, 30 Nov 2018 07:38:39 -0500
parents ce90584be117
children 4301ded2ea50
line wrap: on
line diff
--- a/stacks_gstacks.xml	Thu Nov 29 11:52:48 2018 -0500
+++ b/stacks_gstacks.xml	Fri Nov 30 07:38:39 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="stacks2_gstacks" name="Stacks2: gstacks" version="@WRAPPER_VERSION@">
+<tool id="stacks2_gstacks" name="Stacks2: gstacks" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
     <description>match stacks to a catalog</description>
     <macros>
         <import>macros.xml</import>
@@ -16,7 +16,7 @@
         #set count = len($input_type.input_bam.keys())
     #end if
     #if count == 1:
-        #for $bam in $input_type.input_bam:
+        #for $bam in $input_bam:
             ln -s '$bam' bam_inputs/catalog.bam && 
         #end for
     #else
@@ -176,8 +176,7 @@
     <tests>
         <!-- denovomode, w popmap -->
         <test>
-            <param name="input_type|input_type_selector" value="list"/>
-            <param name="input_type|input_bam">
+            <param name="input_bam">
                 <collection type="list">
                     <element name="PopA_01.matches" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
                     <element name="PopA_02.matches" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />
@@ -196,8 +195,7 @@
         </test>
         <!-- denovomode, wo popmap (allows for only one input), ignore PE, advanced, alt model -->
         <test>
-            <param name="input_type|input_type_selector" value="manual"/>
-            <param name="input_type|input_bam" value="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
+            <param name="input_bam" value="tsv2bam/PopA_01.matches.bam" ftype="bam"/>
             <conditional name="mode_cond">
                 <param name="mode_select" value="denovo" />
                 <param name="ignore_pe_reads" value="--ignore-pe-reads" />
@@ -229,8 +227,7 @@
         </test>
         <!-- refbased wo popmap, paired options, removing all unpaired reads results in an error -->
         <test expect_failure="true" expect_exit_code="1">
-            <param name="input_type|input_type_selector" value="manual"/>
-            <param name="input_type|input_bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
+            <param name="input_bam" value="tsv2bam/PopA_01.matches.bam,tsv2bam/PopA_02.matches.bam"/>
             <conditional name="mode_cond">
                 <param name="mode_select" value="refbased"/>
                 <conditional name="paired_cond">
@@ -249,8 +246,7 @@
         </test>
         <!-- refbased w popmap (here bam names need to be equal to sample names in popmap), \-\-unpaired, advanced, snp model -->
         <test>
-            <param name="input_type|input_type_selector" value="list"/>
-            <param name="input_type|input_bam">
+            <param name="input_bam">
                 <collection type="list">
                     <element name="PopA_01" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
                     <element name="PopA_02" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />
@@ -294,8 +290,7 @@
         </test>
         <!-- refbased wo popmap (here bam names don't matter), \-\-ignorepe -->
         <test>
-            <param name="input_type|input_type_selector" value="list"/>
-            <param name="input_type|input_bam">
+            <param name="input_bam">
                 <collection type="list">
                     <element name="PopA_01.matches" ftype="bam" value="tsv2bam/PopA_01.matches.bam" />
                     <element name="PopA_02.matches" ftype="bam" value="tsv2bam/PopA_02.matches.bam" />