Mercurial > repos > devteam > bwa
comparison bwa-mem.xml @ 13:53646aaaafef draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 3442b18860bc4398d917e3a35943351a9cf031ea
author | devteam |
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date | Mon, 30 Jan 2017 08:49:26 -0500 |
parents | bd3a1e0de84c |
children | 051eba708f43 |
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12:bd3a1e0de84c | 13:53646aaaafef |
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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" label="Select first set of reads" help="Specify dataset with forward reads"/> | 117 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/> |
118 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/> | 118 <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" 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" label="Select fastq dataset" help="Specify dataset with single reads"/> | 126 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" 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" 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" 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" label="Select fastq dataset" help="Specify dataset with interleaved reads"/> | 137 <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" 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> |
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> | 260 </test> |
261 <test> | 261 <test> |
262 <param name="reference_source_selector" value="history" /> | 262 <param name="reference_source_selector" value="history" /> |
263 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | 263 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> |
264 <param name="fastq_input_selector" value="paired"/> | |
265 <param name="fastq_input1" ftype="fastqsanger.gz" value="bwa-mem-fastq1.fq.gz"/> | |
266 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> | |
267 <param name="analysis_type_selector" value="illumina"/> | |
268 <output name="bam_output" ftype="bam" file="bwa-mem-test1.bam" lines_diff="2" /> | |
269 </test> | |
270 <test> | |
271 <param name="reference_source_selector" value="history" /> | |
272 <param name="ref_file" ftype="fasta" value="bwa-mem-mt-genome.fa"/> | |
264 <param name="index_a" value="is"/> | 273 <param name="index_a" value="is"/> |
265 <param name="fastq_input_selector" value="paired"/> | 274 <param name="fastq_input_selector" value="paired"/> |
266 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> | 275 <param name="fastq_input1" ftype="fastqsanger" value="bwa-mem-fastq1.fq"/> |
267 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> | 276 <param name="fastq_input2" ftype="fastqsanger" value="bwa-mem-fastq2.fq"/> |
268 <param name="rg_selector" value="set"/> | 277 <param name="rg_selector" value="set"/> |