Mercurial > repos > iuc > stacks_procrad
comparison stacks_procrad.xml @ 9:57910d476be9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 6ecb1ddafc5575514f9929430e5452027ad02439
| author | iuc |
|---|---|
| date | Sun, 21 May 2017 18:52:17 -0400 |
| parents | bec1f08cdfcc |
| children | be78e39d56b3 |
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| 8:bec1f08cdfcc | 9:57910d476be9 |
|---|---|
| 88 </param> | 88 </param> |
| 89 <when value="single"> | 89 <when value="single"> |
| 90 <param name="input_single" argument="-f" format="fastqsanger,fastqsanger.gz" type="data" label="singles-end reads infile(s)" help="input files" /> | 90 <param name="input_single" argument="-f" format="fastqsanger,fastqsanger.gz" type="data" label="singles-end reads infile(s)" help="input files" /> |
| 91 | 91 |
| 92 <param name="barcode_encoding" type="select" label="Barcode location"> | 92 <param name="barcode_encoding" type="select" label="Barcode location"> |
| 93 <option value="--inline_null" selected="True">Barcode is inline with sequence</option> | 93 <expand macro="barcode_encoding_single" /> |
| 94 <option value="--index_null">Barcode is provided in FASTQ header</option> | |
| 95 </param> | 94 </param> |
| 96 </when> | 95 </when> |
| 97 <when value="paired"> | 96 <when value="paired"> |
| 98 <param name="inputs_paired1" argument="-1" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" /> | 97 <param name="inputs_paired1" argument="-1" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" /> |
| 99 <param name="inputs_paired2" argument="-2" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" /> | 98 <param name="inputs_paired2" argument="-2" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" /> |
| 100 | 99 |
| 101 <param name="barcode_encoding" type="select" label="Barcode location"> | 100 <param name="barcode_encoding" type="select" label="Barcode location"> |
| 102 <option value="--inline_null" selected="True">Barcode is inline with sequence, only on the single-end read (read 1)</option> | 101 <expand macro="barcode_encoding_pair" /> |
| 103 <option value="--index_null">Barcode is provided in FASTQ header, only on the single-end read (read 1)</option> | |
| 104 <option value="--inline_inline">Barcode is inline with sequence, on both single and paired-end read (read 1 and 2)</option> | |
| 105 <option value="--index_index">Barcode is provided in FASTQ header, on both single and paired-end read (read 1 and 2)</option> | |
| 106 <option value="--inline_index">Barcode is inline with sequence on single-end read (read 1), and in FASTQ header for paired-end read (read 2)</option> | |
| 107 <option value="--index_inline">Barcode is provided in FASTQ header on single-end read (read 1), and is inline with sequence on paired-end read (read 2)</option> | |
| 108 </param> | 102 </param> |
| 109 </when> | 103 </when> |
| 110 </conditional> | 104 </conditional> |
| 111 | 105 |
| 112 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" help="Barcode file" /> | 106 <param name="barcode" argument="-b" type="data" format="tabular,txt" label="Barcode file" help="Barcode file" /> |