Mercurial > repos > iuc > stacks_procrad

comparison stacks_procrad.xml @ 9:57910d476be9 draft

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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
comparison
equal deleted inserted replaced
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" />