Mercurial > repos > anmoljh > insilico_read_normalization
changeset 0:60d9e2097e02 draft
Uploaded
| author | anmoljh |
|---|---|
| date | Thu, 27 Aug 2015 09:16:16 -0400 |
| parents | |
| children | f0bd0c42eb2e |
| files | insilico_read_normalization.xml |
| diffstat | 1 files changed, 157 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/insilico_read_normalization.xml Thu Aug 27 09:16:16 2015 -0400 @@ -0,0 +1,157 @@ +<?xml version="1.0"?> +<tool id="insilico_read_nomalization" name="Insilico Read Normalization" version="r20140717"> + +<!-- Written by Anmol J. Hemrom --> +<description>Read Normalization</description> + + <requirements> + <requirement type="package" version="r20140717">trinityrnaseq</requirement> + </requirements> + + +<command interperter="perl"> \$TRINITY_HOME/util/insilico_read_normalization.pl +--JM $JM +--max_cov $maximum_coverage + +## Inputs. +#if str($inputs.paired_or_single) == "paired": + + --left $inputs.left_input --right $inputs.right_input + + #if $inputs.left_input.ext == 'fa': + --seqType fa + #else: + --seqType fq + #end if + + ## Additional parameters. + #if str($inputs.additional_params.use_additional) == "yes": + + #if str($inputs.additional_params.library_type) != "None": + --SS_lib_type $inputs.additional_params.library_type + #end if + + $inputs.additional_params.pairs_together + --CPU $inputs.additional_params.CPU + $inputs.additional_params.PARALLEL_STATS + --KMER_SIZE $inputs.additional_params.KMER_SIZE + --max_pct_stdev $inputs.additional_params.max_pct_stdev + + #end if + + +#else: + + --single $inputs.input + + #if str($inputs.input.ext) == 'fa': + --seqType fa + #else: + --seqType fq + #end if + + ## Additional parameters. + #if str($inputs.additional_params.use_additional) == "yes": + + #if str($inputs.additional_params.library_type) != "None": + --SS_lib_type $inputs.additional_params.library_type + #end if + + ##$inputs.additional_params.pairs_together + --CPU $inputs.additional_params.CPU + ##$inputs.additional_params.PARALLEL_STATS + --KMER_SIZE $inputs.additional_params.KMER_SIZE + --max_pct_stdev $inputs.additional_params.max_pct_stdev + + #end if + +#end if + + + +## direct to output +> $insilico_read_normalization_log 2>&1 + +</command> + + +<inputs> + <param name="JM" type="select" label="JM" help="--JM < string > ; Amount of memory to allocate to Jellyfish for Kmer catalog construction"> + <option value="1G">1G</option> + <option value="10G">10G</option> + <option value="20G">20G</option> + <option value="50G">50G</option> + </param> + + <param name="maximum_coverage" type="integer" value="25" label="Maximum Coverage" help="--max_cov < int > ; targeted maximum coverage for reads"/> + + <conditional name="inputs"> + <param name="paired_or_single" type="select" label="Paired or Single-end data?"> + <option value="paired">Paired</option> + <option value="single">Single</option> + </param> + + <when value="paired"> + <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/> + <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/> + + <conditional name="additional_params"> + <param name="use_additional" type="select" label="Use Additional Params?"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="library_type" type="select" label="Strand-specific Library Type"> + <option value="None">None</option> + <option value="FR">FR</option> + <option value="RF">RF</option> + </param> + <param name="pairs_together" type="boolean" label="--pairs_together" help="process paired reads by averaging stats between pairs and retaining linking info" truevalue="--pairs_together" falsevalue="" checked="true" /> + <param name="CPU" type="integer" value="2" min="1" max="30" label="CPU" help="--CPU < int > ; Number of CPUs to use (Maximum limit is 30 core)" /> + <param name="PARALLEL_STATS" type="boolean" label="--PARALLEL_STATS" help="Generate read stats in parallel for paired reads" truevalue="--PARALLEL_STATS" falsevalue="" checked="true" /> + <param name="KMER_SIZE" type="integer" value="25" label="--KMER SIZE" help="Default is 25" /> + <param name="max_pct_stdev" type="integer" value="200" label="--max_pct_stdev" help="maximum pct of mean for stdev of kmer coverage across read"/> + </when> + </conditional> + </when> + + + <when value="single"> + <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> + + <conditional name="additional_params"> + <param name="use_additional" type="select" label="Use Additional Params?"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="library_type" type="select" label="Strand-specific Library Type"> + <option value="None">None</option> + <option value="F">F</option> + <option value="R">R</option> + </param> + <param name="CPU" type="integer" value="2" min="1" max="30" label="CPU" help="--CPU < int > ; Number of CPUs to use (Maximum limit is 30 core)" /> + <param name="KMER_SIZE" type="integer" value="25" label="--KMER SIZE" help="Default is 25" /> + <param name="max_pct_stdev" type="integer" value="200" label="--max_pct_stdev" help="maximum pct of mean for stdev of kmer coverage across read"/> + </when> + </conditional> + </when> + </conditional> + + +</inputs> + +<outputs> + <data format="txt" name="insilico_read_normalization_log" label="${tool.name} on ${on_string}: log" /> + <data format="fastq" name="left_normalized_read" label="${tool.name} on ${on_string}: Left Read" from_work_dir="left.norm.fq"/> + <data format="fastq" name="right_normalized_read" label="${tool.name} on ${on_string}: Right Read" from_work_dir="right.norm.fq"/> +</outputs> + + +<tests/> +<help>Insilico Read Normalization</help> + +</tool> +