Mercurial > repos > charles > bismark_upgradeproposition

changeset 9:f3e91abe54a2 draft

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Uploaded
author charles
date Mon, 07 Nov 2016 08:12:01 -0500
parents a3477f5888a7
children 7a6c7f9abe75
files bismark/bismark_mapping/bismark_bowtie2_wrapper.xml bismark/tool_dependencies.xml
diffstat 1 files changed, 12 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/bismark/bismark_mapping/bismark_bowtie2_wrapper.xml	Mon Nov 07 08:09:18 2016 -0500
+++ b/bismark/bismark_mapping/bismark_bowtie2_wrapper.xml	Mon Nov 07 08:12:01 2016 -0500
@@ -156,17 +156,17 @@
     <inputs>
         <conditional name="refGenomeSource">
          	<param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
-              <option value="built_in_indexes" selected="true">Use built-in Bismark indexes</option>
-				      <option value="built_in_fasta">Generate Bismark indexes from built-in Reference Genome (fasta)</option>
-              <option value="own_fasta">Generate Bismark indexes from Genome (fasta) in your Galaxy history</option>
+            	<option value="built_in_indexes" selected="true">Use built-in Bismark indexes</option>
+				<option value="built_in_fasta">Generate Bismark indexes from built-in Reference Genome (fasta)</option>
+              	<option value="own_fasta">Generate Bismark indexes from Genome (fasta) in your Galaxy history</option>
          	</param>
         	<when value="built_in_indexes">
-				    <param name="built_in_indexes" type="select" label="Select Reference Genome (bismark indexes)" help="If your genome of interest is not listed, contact your Galaxy admin">
-              <options from_data_table="bismark_indexes">
-                <filter type="sort_by" column="name"/>
-						    <validator type="no_options" message="No indexes are available for the selected input dataset"/>
-              </options>
-				    </param>
+				<param name="built_in_indexes" type="select" label="Select Reference Genome (bismark indexes)" help="If your genome of interest is not listed, contact your Galaxy admin">
+              		<options from_data_table="bismark_indexes">
+                		<filter type="sort_by" column="name"/>
+						<validator type="no_options" message="No indexes are available for the selected input dataset"/>
+              		</options>
+				</param>
           </when>
           <when value="built_in_fasta"> 
             <param name="built_in_fasta" type="select" label="Select Reference Genome (fasta)">
@@ -247,8 +247,9 @@
         <data format="txt" name="report_file" label="${tool.name} on ${on_string}: mapping report">
             <filter>
             ((
-                params['settingsType'] == "custom" and
-                params['isReportOutput'] is True
+            	params['settingsType'] == "default" or
+                ( params['settingsType'] == "custom" and
+                params['isReportOutput'] is True )
             ))
             </filter>
         </data>