Mercurial > repos > iuc > gatk2

diff variant_select.xml @ 13:669a23f1f4b5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit e5a5ad091c621348dc6ce2df861475ebc54a380e
author iuc
date Tue, 13 Oct 2015 17:22:38 -0400
parents 0d369d08ad6e
children
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--- a/variant_select.xml	Thu May 14 22:47:18 2015 -0400
+++ b/variant_select.xml	Tue Oct 13 17:22:38 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="gatk2_variant_select" name="Select Variants" version="@VERSION@.0">
+<tool id="gatk2_variant_select" name="Select Variants" version="@VERSION@.2">
   <description>from VCF files</description>
   <macros>
     <import>gatk2_macros.xml</import>
@@ -50,12 +50,12 @@
     ##start tool specific options
     #if str( $analysis_param_type.analysis_param_type_selector ) == 'advanced':
         -p '
-          #for $exclude_sample_file in $analysis_param_type.exclude_sample_file_repeat:
-              --exclude_sample_file "${exclude_sample_file.exclude_sample_file}"
+          #for $esf in $analysis_param_type.exclude_sample_file:
+              --exclude_sample_file "${esf}"
           #end for
 
-          #for $sample_file in $analysis_param_type.sample_file_repeat:
-              --sample_file "${ample_file.sample_file}"
+          #for $sf in $analysis_param_type.sample_file:
+              --sample_file "${sf}"
           #end for
 
           #if $analysis_param_type.input_keep_ids:
@@ -143,15 +143,11 @@
 
     <expand macro="analysis_type_conditional">
 
-        <repeat name="exclude_sample_file_repeat" title="Exclude Samples by file" help="-xl_sf,--exclude_sample_file &amp;lt;exclude_sample_file&amp;gt;">
-            <param name="exclude_sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to exclude"/>
-        </repeat>
+        <param name="exclude_sample_file" type="data" format="txt" multiple="True" label="Exclude Samples by file" help="File containing a list of samples (one per line) to exclude (-xl_sf,--exclude_sample_file &amp;lt;exclude_sample_file&amp;gt;)"/>
 
-        <repeat name="sample_file_repeat" title="Samples by file" help="-sf,--sample_file &amp;lt;sample_file&amp;gt;">
-            <param name="sample_file" type="data" format="txt" label="File containing a list of samples (one per line) to include" />
-        </repeat>
+        <param name="sample_file" type="data" format="txt" multiple="True" label="Samples by file"  help="File containing a list of samples (one per line) to include (-sf,--sample_file &amp;lt;sample_file&amp;gt;)"/>
 
-        <param name="input_keep_ids" type="data" format="text" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &amp;lt;keepIDs&amp;gt;"/>
+        <param name="input_keep_ids" type="data" format="txt" label="Only emit sites whose ID is found in this file" optional="True" help="-IDs,--keepIDs &amp;lt;keepIDs&amp;gt;"/>
 
         <param name="keep_original_AC" type="boolean" truevalue="--keepOriginalAC" falsevalue="" label="Don't update the AC, AF, or AN values in the INFO field after selecting" help="-keepOriginalAC,--keepOriginalAC" />