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comparison bwa-mem.xml @ 14:051eba708f43 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 33c17fa6a2d8c15972d93031b2ca4182cdf31439
author devteam
date Thu, 01 Jun 2017 11:38:47 -0400
parents 53646aaaafef
children 4d82cf59895e
comparison
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13:53646aaaafef 14:051eba708f43
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.1"> 2 <tool id="bwa_mem" name="Map with BWA-MEM" version="@VERSION@.2">
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>
112 <option value="single">Single</option> 112 <option value="single">Single</option>
113 <option value="paired_collection">Paired Collection</option> 113 <option value="paired_collection">Paired Collection</option>
114 <option value="paired_iv">Paired Interleaved</option> 114 <option value="paired_iv">Paired Interleaved</option>
115 </param> 115 </param>
116 <when value="paired"> 116 <when value="paired">
117 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/> 117 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>
118 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/> 118 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
119 <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."> 119 <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.">
120 <sanitizer invalid_char=""> 120 <sanitizer invalid_char="">
121 <valid initial="string.digits"><add value=","/> </valid> 121 <valid initial="string.digits"><add value=","/> </valid>
122 </sanitizer> 122 </sanitizer>
123 </param> 123 </param>
124 </when> 124 </when>
125 <when value="single"> 125 <when value="single">
126 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with single reads"/> 126 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
127 </when> 127 </when>
128 <when value="paired_collection"> 128 <when value="paired_collection">
129 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/> 129 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
130 <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."> 130 <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.">
131 <sanitizer invalid_char=""> 131 <sanitizer invalid_char="">
132 <valid initial="string.digits"><add value=","/> </valid> 132 <valid initial="string.digits"><add value=","/> </valid>
133 </sanitizer> 133 </sanitizer>
134 </param> 134 </param>
135 </when> 135 </when>
136 <when value="paired_iv"> 136 <when value="paired_iv">
137 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> 137 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
138 <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."> 138 <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.">
139 <sanitizer invalid_char=""> 139 <sanitizer invalid_char="">
140 <valid initial="string.digits"><add value=","/> </valid> 140 <valid initial="string.digits"><add value=","/> </valid>
141 </sanitizer> 141 </sanitizer>
142 </param> 142 </param>
255 <param name="fastq_input_selector" value="paired"/> 255 <param name="fastq_input_selector" value="paired"/>
256 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> 256 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/>
257 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> 257 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/>
258 <param name="analysis_type_selector" value="illumina"/> 258 <param name="analysis_type_selector" value="illumina"/>
259 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" /> 259 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" />
260 </test>
261 <test>
262 <param name="reference_source_selector" value="history" />
263 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
264 <param name="fastq_input_selector" value="single"/>
265 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fasta1.fa"/>
266 <param name="analysis_type_selector" value="illumina"/>
267 <output name="bam_output" ftype="bam" file="bwa-mem-test1-fasta.bam" lines_diff="2" />
260 </test> 268 </test>
261 <test> 269 <test>
262 <param name="reference_source_selector" value="history" /> 270 <param name="reference_source_selector" value="history" />
263 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> 271 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/>
264 <param name="fastq_input_selector" value="paired"/> 272 <param name="fastq_input_selector" value="paired"/>