Mercurial > repos > tiagoantao > clone_filter
view STACKS_clone_filter.xml @ 7:2059c028c07a draft
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author | tiagoantao |
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date | Thu, 04 Feb 2016 08:00:32 -0500 |
parents | c50b7a3ff5ad |
children | a8b87bc0c3ad |
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<tool id="STACKS_clone_filter" name="STACKS: clone_filter" version="0.9.0"> <description>Run the STACKS clone_filter program</description> <requirements> <requirement type="package" version="1.18">stacks</requirement> </requirements> <stdio> <exit_code range="1" level="fatal" description="Error in Stacks clone_filter" /> </stdio> <command interpreter="python"> STACKS_clone_filter.py #if $data_type.dt_select == 'single': -f $data_type.fname #else -fwd $data_type.fwd -rev $data_type.rev #end if $oligo_options #if $oligo_len_1 > -1: --oligo_len_1 $oligo_len_1 #end if #if $oligo_len_2 > -1: --oligo_len_2 $oligo_len_2 #end if </command> <inputs> <conditional name="data_type"> <param name="dt_select" type="select" label="Single or Paired-end"> <option value="single">Single</option> <option value="pair">Pair</option> </param> <when value="single"> <param name="fname" type="data" format="fastq" label="FASTQ" /> </when> <when value="pair"> <param name="fwd" type="data" format="fastq" label="Forward FASTQ" /> <param name="rev" type="data" format="fastq" label="Reverse FASTQ" /> </when> </conditional> <param name="oligo_len_1" type="integer" label="length of the single-end oligo sequence in data set (-1 == ignore)"/> <param name="oligo_len_2" type="integer" label="length of the paired-end oligo sequence in data set (-1 == ignore)"/> <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> <data format="fastq" name="clean" from_work_dir="job_outputs/clean.fq"> <filter>data_type['dt_select'] == 'single' </filter> </data> <data format="fastq" name="clean_fwd" from_work_dir="job_outputs/fwd.fq"> <filter>data_type['dt_select'] == 'pair' </filter> </data> <data format="fastq" name="clean_rev" from_work_dir="job_outputs/rev.fq"> <filter>data_type['dt_select'] == 'pair' </filter> </data> </outputs> <tests> <test> <param name="dt_select" value="pair" /> <param name="fwd" value="fwd.fq" /> <param name="rev" value="rev.fq" /> <output name="clean_fwd" /> <output name="clean_rev" /> </test> </tests> <help> -------- **Project links:** `STACKS website <http://creskolab.uoregon.edu/stacks/>`_ . `STACKS manual <http://creskolab.uoregon.edu/stacks/stacks_manual.pdf>`_ . `STACKS google group <https://groups.google.com/forum/#!forum/stacks-users>`_ . </help> <citations> <citation type="doi">10.1111/mec.12354</citation> <citation type="doi">10.1111/mec.12330</citation> <citation type="doi">10.1534/g3.111.000240</citation> <citation type="doi">10.1534/genetics.111.127324</citation> <citation type="doi">10.1111/j.1755-0998.2010.02967.x</citation> <citation type="doi">10.1073/pnas.1006538107</citation> </citations> </tool>