Mercurial > repos > matthias > stacks2_gstacks

changeset 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
files macros.xml stacks_gstacks.xml
diffstat 2 files changed, 12 insertions(+), 27 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Thu Nov 29 11:52:48 2018 -0500
+++ b/macros.xml	Fri Nov 30 07:38:39 2018 -0500
@@ -2,12 +2,13 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="@WRAPPER_VERSION@">stacks</requirement>
+            <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>
             <yield/>
         </requirements>
     </xml>
 
-    <token name="@WRAPPER_VERSION@">2.2=he860b03_0</token>
+    <token name="@STACKS_VERSION@">2.2</token>
+    <token name="@WRAPPER_VERSION@">1</token>
 
     <xml name="stdio">
         <stdio>
@@ -174,22 +175,11 @@
 
     <!-- macro and token for BAM input-->
     <xml name="bam_input_macro">
-        <conditional name="input_type">
-            <param name="input_type_selector" type="select" label="BAM files">
-                <option value="list">data set list</option>
-                <option value="manual">data sets</option>
-            </param>
-            <when value="manual">
-                <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" />
-            </when>
-            <when value="list">
-                <param name="input_bam" format="bam" type="data_collection" collection_type="list" label="BAM files" />
-            </when>
-        </conditional>
+        <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="BAM files" />
     </xml>
     <token name="@BAM_INPUT@"><![CDATA[
     #set $bamlist = ""
-    #for $bam in $input_type.input_bam:
+    #for $bam in $input_bam:
         #set $filename = $clean_ext($bam.element_identifier)+".bam"
         #if re.search('.*\.bam$', $filename)
             ln -s '$bam' bam_inputs/$filename &&
--- a/stacks_gstacks.xml	Thu Nov 29 11:52:48 2018 -0500
+++ b/stacks_gstacks.xml	Fri Nov 30 07:38:39 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="stacks2_gstacks" name="Stacks2: gstacks" version="@WRAPPER_VERSION@">
+<tool id="stacks2_gstacks" name="Stacks2: gstacks" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
     <description>match stacks to a catalog</description>
     <macros>
         <import>macros.xml</import>
@@ -16,7 +16,7 @@
         #set count = len($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" />