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comparison 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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2:82fb5e3bb93e 3:0d18a3ba2d1c
1 <tool id="breseq" name="breseq" version="@PACKAGE_VERSION@+@GALAXY_VERSION@"> 1 <tool id="breseq" name="breseq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2
3 <description>find mutations in haploid microbial genomes</description> 2 <description>find mutations in haploid microbial genomes</description>
4 3 <xrefs>
4 <xref type="bio.tools">breseq</xref>
5 </xrefs>
5 <macros> 6 <macros>
6 <import>macros.xml</import> 7 <import>macros.xml</import>
7 </macros> 8 </macros>
8 9
9 <requirements> 10 <requirements>
10 <requirement type="package" version="0.35.5">breseq</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">breseq</requirement>
11 <requirement type="package" version="1.32">tar</requirement> 12 <requirement type="package" version="1.32">tar</requirement>
12 </requirements> 13 </requirements>
13 14
14 <version_command>breseq --version</version_command> 15 <version_command>breseq --version</version_command>
15 16
140 <param name="name" argument="--name" type="text" value="" label="Analysis Name" help="Human-readable name of the analysis run for output (DEFAULT=none)." /> 141 <param name="name" argument="--name" type="text" value="" label="Analysis Name" help="Human-readable name of the analysis run for output (DEFAULT=none)." />
141 142
142 <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." /> 143 <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." />
143 144
144 <section name="output_options" title="Output Options" expanded="false"> 145 <section name="output_options" title="Output Options" expanded="false">
145 <param name="formats" type="select" multiple="true" optional="false" display="checkboxes" label="Output Formats"> 146 <param name="formats" type="select" multiple="true" optional="false" label="Output Formats">
146 <option value="gd" selected="true">Variants (GenomeDiff)</option> 147 <option value="gd" selected="true">Variants (GenomeDiff)</option>
147 <option value="html">Variant Report (Webpage)</option> 148 <option value="html">Variant Report (Webpage)</option>
148 <option value="zip">All Variant Results (Gzip)</option> 149 <option value="zip">All Variant Results (Gzip)</option>
149 <option value="log">Log (Text)</option> 150 <option value="log">Log (Text)</option>
150 </param> 151 </param>
265 <param name="own_genome" value="lambda.gbk" /> 266 <param name="own_genome" value="lambda.gbk" />
266 </conditional> 267 </conditional>
267 </repeat> 268 </repeat>
268 <conditional name="run"> 269 <conditional name="run">
269 <param name="mode" value="annotate" /> 270 <param name="mode" value="annotate" />
270 <param name="gds" value="gdout.txt" /> 271 <param name="gds" value="gdout.txt" ftype="tabular" />
271 <section name="output_options"> 272 <section name="output_options">
272 <param name="formats" value="html" /> 273 <param name="formats" value="html" />
273 </section> 274 </section>
274 </conditional> 275 </conditional>
275 276