Mercurial > repos > devteam > bwa
comparison bwa-mem.xml @ 4:774491f4a074 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 33c17fa6a2d8c15972d93031b2ca4182cdf31439
| author | devteam |
|---|---|
| date | Thu, 01 Jun 2017 11:38:11 -0400 |
| parents | 0bde88ff668c |
| children | b59a6178a6e0 |
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| 3:0bde88ff668c | 4:774491f4a074 |
|---|---|
| 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 (> 100 bp) against reference genome</description> | 3 <description>- map medium and long reads (> 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 "250" and "250,25" will work while "250,,10" 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 "250" and "250,25" will work while "250,,10" 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 "250" and "250,25" will work while "250,,10" 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 "250" and "250,25" will work while "250,,10" 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 "250" and "250,25" will work while "250,,10" 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 "250" and "250,25" will work while "250,,10" 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"/> |