Mercurial > repos > tiagoantao > clone_filter
diff 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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--- a/STACKS_clone_filter.xml Wed Feb 03 10:58:13 2016 -0500 +++ b/STACKS_clone_filter.xml Thu Feb 04 07:50:26 2016 -0500 @@ -34,6 +34,17 @@ <param name="rev" type="data" format="fastq" label="Reverse FASTQ" /> </when> </conditional> + <param name="oligo_len_1" type="int" label="length of the single-end oligo sequence in data set"/> + <param name="oligo_len_2" type="int" label="length of the paired-end oligo sequence in data set"/> + <param name="oligo_options" type="select" label="Oligo sequence options"> + <option value="inline_null" selected="true">random oligo is inline with sequence, occurs only on single-end read</option> + <option value="null_index">random oligo is provded in FASTQ header (Illumina i7 read if both i5 and i7 read are provided).</option> + <option value="index_null">random oligo is provded in FASTQ header (Illumina i5 or i7 read)</option> + <option value="inline_inline">random oligo is inline with sequence, occurs on single and paired-end read</option> + <option value="index_index">random oligo is provded in FASTQ header (Illumina i5 and i7 read)</option> + <option value="inline_index">random oligo is inline with sequence on single-end read and second oligo occurs in FASTQ header</option> + <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> + </param> </inputs> <outputs>