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comparison bwa-mem.xml @ 7:d8c9597bfb09 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit ddb8bdb9d62399f086b06b3469450d0aad2113bd
author devteam
date Tue, 03 Nov 2015 09:36:45 -0500
parents 09a7281d24c5
children 7bee165c3a44
comparison
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6:09a7281d24c5 7:d8c9597bfb09
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bwa_mem" name="Map with BWA-MEM" version="0.3.1"> 2 <tool id="bwa_mem" name="Map with BWA-MEM" version="0.4.1">
3 <description>- map medium and long reads (&gt; 100 bp) against reference genome</description> 3 <description>- map medium and long reads (&gt; 100 bp) against reference genome</description>
4 <macros> 4 <macros>
5 <import>read_group_macros.xml</import> 5 <import>read_group_macros.xml</import>
6 <import>bwa_macros.xml</import> 6 <import>bwa_macros.xml</import>
7 </macros> 7 </macros>
8 <requirements> 8 <expand macro="requirements" />
9 <requirement type="package" version="0.7.10.039ea20639">bwa</requirement>
10 <requirement type="package" version="1.1">samtools</requirement>
11 </requirements>
12 <expand macro="stdio" /> 9 <expand macro="stdio" />
13 <command> 10 <command>
14 #set $reference_fasta_filename = "localref.fa" 11 #set $reference_fasta_filename = "localref.fa"
15 12
16 #if str( $reference_source.reference_source_selector ) == "history": 13 #if str( $reference_source.reference_source_selector ) == "history":
168 <option value="paired_iv">Paired Interleaved</option> 165 <option value="paired_iv">Paired Interleaved</option>
169 </param> 166 </param>
170 <when value="paired"> 167 <when value="paired">
171 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/> 168 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
172 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/> 169 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
173 <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details."> 170 <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
174 <sanitizer invalid_char=""> 171 <sanitizer invalid_char="">
175 <valid initial="string.digits"><add value=","/> </valid> 172 <valid initial="string.digits"><add value=","/> </valid>
176 </sanitizer> 173 </sanitizer>
177 </param> 174 </param>
178 </when> 175 </when>
179 <when value="single"> 176 <when value="single">
180 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/> 177 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>
181 </when> 178 </when>
182 <when value="paired_collection"> 179 <when value="paired_collection">
183 <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> 180 <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
184 <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details."> 181 <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
185 <sanitizer invalid_char=""> 182 <sanitizer invalid_char="">
186 <valid initial="string.digits"><add value=","/> </valid> 183 <valid initial="string.digits"><add value=","/> </valid>
187 </sanitizer> 184 </sanitizer>
188 </param> 185 </param>
189 </when> 186 </when>
190 <when value="paired_iv"> 187 <when value="paired_iv">
191 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> 188 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
192 <param name="iset_stats" type="text" optional="True" size="10" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details."> 189 <param name="iset_stats" type="text" optional="True" label="Enter mean, standard deviation, max, and min for insert lengths." help="-I; This parameter is only used for paired reads. Only mean is required while sd, max, and min will be inferred. Examples: both &quot;250&quot; and &quot;250,25&quot; will work while &quot;250,,10&quot; will not. See below for details.">
193 <sanitizer invalid_char=""> 190 <sanitizer invalid_char="">
194 <valid initial="string.digits"><add value=","/> </valid> 191 <valid initial="string.digits"><add value=","/> </valid>
195 </sanitizer> 192 </sanitizer>
196 </param> 193 </param>
197 </when> 194 </when>