Mercurial > repos > devteam > freebayes

diff macros.xml @ 28:977a5301b66d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 9bbda385129b4bc34f66889d28c2570bf5bb2214
author iuc
date Tue, 06 Jun 2017 18:41:18 -0400
parents 9f164587a92f
children 156b60c1530f
line wrap: on
line diff
--- a/macros.xml	Tue Jun 06 11:44:38 2017 -0400
+++ b/macros.xml	Tue Jun 06 18:41:18 2017 -0400
@@ -1,6 +1,12 @@
 <macros>
     <token name="@DEPENDENCY_VERSION@">1.1.0</token>
-
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@DEPENDENCY_VERSION@">freebayes</requirement>
+            <requirement type="package" version="0.1.19">samtools</requirement>
+            <yield />
+        </requirements>
+    </xml>
     <xml name="citations">
         <citations>
             <citation type="bibtex">
@@ -20,24 +26,23 @@
     </xml>
     <xml name="input_bam">
         <conditional name="batchmode">
-            <param name="processmode" type="select" label="Run in batch mode?" help="Selecting individual mode will generate one VCF file for each input BAM file. Selecting the merge option will produce one VCF file for all input BAM files." display="radio">
-                <option value="individual" selected="True">Run individually</option>
+            <param name="processmode" type="select" label="Run in batch mode?" help="Selecting individual mode will generate one VCF dataset for each input BAM dataset. Selecting the merge option will produce one VCF dataset for all input BAM datasets" display="radio">
+                <option value="individual" selected="true">Run individually</option>
                 <option value="merge">Merge output VCFs</option>
             </param>
             <when value="individual">
-                <param name="input_bams" type="data" format="bam" label="BAM file">
+                <param name="input_bams" type="data" format="bam" label="BAM dataset">
                     <yield />
                 </param>
             </when>
             <when value="merge">
-                <param name="input_bams" type="data" format="bam" multiple="True" label="BAM file">
+                <param name="input_bams" type="data" format="bam" multiple="true" label="BAM dataset(s)">
                     <yield />
                 </param>
             </when>
         </conditional>
     </xml>
     <xml name="par_min_cov">
-        <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site"
-               help="default=0" argument="--coverage" />
+        <param name="min_coverage" argument="--coverage" type="integer" value="0" label="Require at least this coverage to process a site" />
     </xml>
 </macros>