Mercurial > repos > tiagoantao > clone_filter
comparison STACKS_clone_filter.xml @ 5:1a5ebb16aaea draft
planemo upload commit 4d00a0b7a4b859b642eceb3c7cd4adb1453903a0-dirty
| author | tiagoantao |
|---|---|
| date | Thu, 04 Feb 2016 07:50:26 -0500 |
| parents | f4b429a3494a |
| children | c50b7a3ff5ad |
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| 4:f4b429a3494a | 5:1a5ebb16aaea |
|---|---|
| 32 <when value="pair"> | 32 <when value="pair"> |
| 33 <param name="fwd" type="data" format="fastq" label="Forward FASTQ" /> | 33 <param name="fwd" type="data" format="fastq" label="Forward FASTQ" /> |
| 34 <param name="rev" type="data" format="fastq" label="Reverse FASTQ" /> | 34 <param name="rev" type="data" format="fastq" label="Reverse FASTQ" /> |
| 35 </when> | 35 </when> |
| 36 </conditional> | 36 </conditional> |
| 37 <param name="oligo_len_1" type="int" label="length of the single-end oligo sequence in data set"/> | |
| 38 <param name="oligo_len_2" type="int" label="length of the paired-end oligo sequence in data set"/> | |
| 39 <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> | |
| 41 <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> | |
| 43 <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> | |
| 45 <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> | |
| 47 </param> | |
| 37 </inputs> | 48 </inputs> |
| 38 | 49 |
| 39 <outputs> | 50 <outputs> |
| 40 <data format="fastq" name="clean" from_work_dir="job_outputs/clean.fq"> | 51 <data format="fastq" name="clean" from_work_dir="job_outputs/clean.fq"> |
| 41 <filter>data_type['dt_select'] == 'single' </filter> | 52 <filter>data_type['dt_select'] == 'single' </filter> |