Mercurial > repos > iuc > breseq

diff breseq.xml @ 3:0d18a3ba2d1c draft default tip

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"planemo upload commit 6e869b3e13ed7b012b270f14fce812613642e5f2"
author iuc
date Mon, 04 Apr 2022 08:30:52 +0000
parents 82fb5e3bb93e
children
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--- a/breseq.xml	Wed Apr 07 12:17:45 2021 +0000
+++ b/breseq.xml	Mon Apr 04 08:30:52 2022 +0000
@@ -1,13 +1,14 @@
-<tool id="breseq" name="breseq" version="@PACKAGE_VERSION@+@GALAXY_VERSION@">
-
+<tool id="breseq" name="breseq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>find mutations in haploid microbial genomes</description>
-
+    <xrefs>
+        <xref type="bio.tools">breseq</xref>
+    </xrefs>
     <macros>
         <import>macros.xml</import>
     </macros>
 
     <requirements>
-        <requirement type="package" version="0.35.5">breseq</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">breseq</requirement>
         <requirement type="package" version="1.32">tar</requirement>
     </requirements>
 
@@ -142,7 +143,7 @@
                 <param name="predict_junctions" type="boolean" truevalue="" falsevalue="--no-junction-prediction" checked="true" label="Predict Junctions" help="Predict new sequence junctions (default).  --no-junction-prediction is supplied if 'No' is selected.  Otherwise, there is no flag." />
 
                 <section name="output_options" title="Output Options" expanded="false">
-                    <param name="formats" type="select" multiple="true" optional="false" display="checkboxes" label="Output Formats">
+                    <param name="formats" type="select" multiple="true" optional="false" label="Output Formats">
                         <option value="gd" selected="true">Variants (GenomeDiff)</option>
                         <option value="html">Variant Report (Webpage)</option>
                         <option value="zip">All Variant Results (Gzip)</option>
@@ -267,7 +268,7 @@
             </repeat>
             <conditional name="run">
                 <param name="mode" value="annotate" />
-                <param name="gds" value="gdout.txt" />
+                <param name="gds" value="gdout.txt" ftype="tabular" />
                 <section name="output_options">
                     <param name="formats" value="html" />
                 </section>