Mercurial > repos > tiagoantao > clone_filter
diff STACKS_clone_filter.xml @ 0:42e64fbf4609 draft
planemo upload commit 60a090d1dc89c2eb383feeb35cd6078b9130e0e5-dirty
author | tiagoantao |
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date | Tue, 02 Feb 2016 21:15:50 -0500 |
parents | |
children | b91ab894f6e0 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/STACKS_clone_filter.xml Tue Feb 02 21:15:50 2016 -0500 @@ -0,0 +1,81 @@ +<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 + -1 $data_type.fwd + -2 $data_type.rev +#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="fastq" label="FASTQ" /> + </when> + <when value="pair"> + <param name="fwd" type="fastq" label="Forward FASTQ" /> + <param name="rev" type="fastq" label="Reverse FASTQ" /> + </when> + </conditional> +</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>