Mercurial > repos > tiagoantao > clone_filter

comparison STACKS_clone_filter.xml @ 8:a8b87bc0c3ad draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty
author tiagoantao
date Thu, 04 Feb 2016 08:13:32 -0500
parents 2059c028c07a
children 89b911668f1d
comparison
equal deleted inserted replaced
7:2059c028c07a 8:a8b87bc0c3ad
16 -f $data_type.fname 16 -f $data_type.fname
17 #else 17 #else
18 -fwd $data_type.fwd 18 -fwd $data_type.fwd
19 -rev $data_type.rev 19 -rev $data_type.rev
20 #end if 20 #end if
21 $oligo_options 21 -opt $oligo_option
22 #if $oligo_len_1 > -1: 22 #if $oligo_len_1 > -1:
23 --oligo_len_1 $oligo_len_1 23 --oligo_len_1 $oligo_len_1
24 #end if 24 #end if
25 #if $oligo_len_2 > -1: 25 #if $oligo_len_2 > -1:
26 --oligo_len_2 $oligo_len_2 26 --oligo_len_2 $oligo_len_2
42 </when> 42 </when>
43 </conditional> 43 </conditional>
44 <param name="oligo_len_1" type="integer" label="length of the single-end oligo sequence in data set (-1 == ignore)"/> 44 <param name="oligo_len_1" type="integer" label="length of the single-end oligo sequence in data set (-1 == ignore)"/>
45 <param name="oligo_len_2" type="integer" label="length of the paired-end oligo sequence in data set (-1 == ignore)"/> 45 <param name="oligo_len_2" type="integer" label="length of the paired-end oligo sequence in data set (-1 == ignore)"/>
46 <param name="oligo_options" type="select" label="Oligo sequence options"> 46 <param name="oligo_options" type="select" label="Oligo sequence options">
47 <option value="--inline_null" selected="true">random oligo is inline with sequence, occurs only on single-end read</option> 47 <option value="inline_null" selected="true">random oligo is inline with sequence, occurs only on single-end read</option>
48 <option value="--null_index">random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).</option> 48 <option value="null_index">random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).</option>
49 <option value="--index_null">random oligo is provded in FASTQ header (Illumina i5 or i7 read)</option> 49 <option value="index_null">random oligo is provded in FASTQ header (Illumina i5 or i7 read)</option>
50 <option value="--inline_inline">random oligo is inline with sequence, occurs on single and paired-end read</option> 50 <option value="inline_inline">random oligo is inline with sequence, occurs on single and paired-end read</option>
51 <option value="--index_index">random oligo is provded in FASTQ header (Illumina i5 and i7 read)</option> 51 <option value="index_index">random oligo is provded in FASTQ header (Illumina i5 and i7 read)</option>
52 <option value="inline_index">random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header</option> 52 <option value="inline_index">random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header</option>
53 <option value="index_inline">random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data)</option> 53 <option value="index_inline">random oligo occurs in FASTQ header (Illumina i5 or i7 read) and is inline with sequence on single-end read (if single read data) or paired-end read (if paired data)</option>
54 </param> 54 </param>
55 </inputs> 55 </inputs>
56 56