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comparison STACKS_clone_filter.xml @ 7:2059c028c07a draft

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planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty
author tiagoantao
date Thu, 04 Feb 2016 08:00:32 -0500
parents c50b7a3ff5ad
children a8b87bc0c3ad
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6:c50b7a3ff5ad 7:2059c028c07a
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
22 #if $oligo_len_1 > -1:
23 --oligo_len_1 $oligo_len_1
24 #end if
25 #if $oligo_len_2 > -1:
26 --oligo_len_2 $oligo_len_2
27 #end if
21 </command> 28 </command>
22 29
23 <inputs> 30 <inputs>
24 <conditional name="data_type"> 31 <conditional name="data_type">
25 <param name="dt_select" type="select" label="Single or Paired-end"> 32 <param name="dt_select" type="select" label="Single or Paired-end">
32 <when value="pair"> 39 <when value="pair">
33 <param name="fwd" type="data" format="fastq" label="Forward FASTQ" /> 40 <param name="fwd" type="data" format="fastq" label="Forward FASTQ" />
34 <param name="rev" type="data" format="fastq" label="Reverse FASTQ" /> 41 <param name="rev" type="data" format="fastq" label="Reverse FASTQ" />
35 </when> 42 </when>
36 </conditional> 43 </conditional>
37 <param name="oligo_len_1" type="integer" label="length of the single-end oligo sequence in data set"/> 44 <param name="oligo_len_1" type="integer" label="length of the single-end oligo sequence in data set (-1 == ignore)"/>
38 <param name="oligo_len_2" type="integer" label="length of the paired-end oligo sequence in data set"/> 45 <param name="oligo_len_2" type="integer" label="length of the paired-end oligo sequence in data set (-1 == ignore)"/>
39 <param name="oligo_options" type="select" label="Oligo sequence options"> 46 <param name="oligo_options" type="select" label="Oligo sequence options">
40 <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>
41 <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>
42 <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>
43 <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>
44 <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>
45 <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>
46 <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>
47 </param> 54 </param>
48 </inputs> 55 </inputs>
49 56