Mercurial > repos > badger > trinityrnaseq
diff trinityrnaseq_norm.xml @ 14:961b5bf3fcc8 draft default tip
remove other tools
| author | Eric Badger <badger@msi.umn.edu> |
|---|---|
| date | Tue, 08 Apr 2014 13:16:06 -0500 |
| parents | 6425d1da3746 |
| children |
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--- a/trinityrnaseq_norm.xml Fri Apr 04 15:30:44 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,178 +0,0 @@ -<tool id="trinityrnaseq_norm" name="Trinity read normalization" version="0.0.2"> - <!-- Written by Jeremy Goecks, modified by Josh Bowden for normalization proceedure, now maintained here by bhaas --> - <description>Pre-process RNA-seq data to reduce coverage of highly covered areas</description> - <requirements> - <requirement type="package" version="2013_08_14">trinityrnaseq</requirement> - </requirements> - <command> - ## symlink input in work_dir - #if str($inputs.paired_or_single) == "paired": - ln -s $inputs.left_input left_reads && - ln -s $inputs.right_input right_reads && - #else: - ln -s $inputs.input single_reads && - #end if - \${TRINITY_HOME}/util/normalize_by_kmer_coverage.pl --JM $JM --max_cov $max_cov - ## Inputs. - #if str($inputs.paired_or_single) == "paired": - --left left_reads --right right_reads - #if $inputs.left_input.ext == 'fa': - --seqType fa - #else: - --seqType fq - #end if - $inputs.pe_reads_unordered - #if str($inputs.library_type) != "None": - --SS_lib_type $inputs.library_type - #end if - $inputs.pairs_together - $inputs.parallel_stats - #else: - --single single_reads - #if str($inputs.input.ext) == 'fa': - --seqType fa - #else: - --seqType fq - #end if - #if str($inputs.library_type) != "None": - --SS_lib_type $inputs.library_type - #end if - #end if - #if $kmer_size: - --KMER_SIZE $kmer_size - #end if - #if $max_pct_stdev: - --max_pct_stdev $max_pct_stdev - #end if - ## direct stdio to output - | tee $trinity_coverage_normalization_log && - #if str($inputs.paired_or_single) == "paired": - cp left_reads.normalized* $output_left && - cp right_reads.normalized* $output_right - #else: - cp single_reads.normalized* $output_single - #end if - </command> - <inputs> - <param name="JM" type="select" label="JM" help="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> - <option value="100G">100G</option> - </param> - - <param name="max_cov" type="select" label="max_cov" help="Read coverage in terms of maximum covarge to keep"> - <option value="30">30</option> - <option value="40">40</option> - <option value="50">50</option> - <option value="60">60</option> - <option value="70">70</option> - <option value="100">100</option> - </param> - - <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=""/> - <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="pe_reads_unordered" type="boolean" truevalue="--PE_reads_unordered" falsevalue="" checked="false" label="set if the input paired-end reads are not identically ordered"/> - <param name="pairs_together" type="boolean" truevalue="--pairs_together" falsevalue="" checked="false" label="process paired reads by averaging stats between pairs and retaining linking info"/> - <param name="parallel_stats" type="boolean" truevalue="--PARALLEL_STATS" falsevalue="" checked="false" label="generate read stats in parallel for paired reads" help="(Figure 2X Inchworm memory requirement)"/> - </when> - <when value="single"> - <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/> - <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> - </when> - </conditional> - <param name="kmer_size" type="integer" value="" optional="true" label="KMER SIZE" help="default: 25"> - <validator type="in_range" message="kmer size between 3 and 200" min="3" max="200"/> - </param> - <param name="max_pct_stdev" type="integer" value="" optional="true" label="maximum pct of mean for stdev of kmer coverage across read" help="default: 100"> - <validator type="in_range" message="kmer size between 10 and 100" min="10" max="100"/> - </param> - - </inputs> - <stdio> - <exit_code range="1:" level="fatal" description="Failed" /> - <regex match="Error" - source="stdout" - level="fatal" - description="Failed" /> - </stdio> - <outputs> - <!-- I have not found a way to do condional outputs so all potential output files are specified and some will be empty --> - <data format="txt" name="trinity_coverage_normalization_log" label="${tool.name} on ${on_string}: log" /> - <data format_source="left_input" name="output_left" label="${tool.name} on ${on_string}: Normalized left reads"> - <filter>inputs['paired_or_single'] == "paired"</filter> - </data> - <data format_source="right_input" name="output_right" label="${tool.name} on ${on_string}: Normalized right reads"> - <filter>inputs['paired_or_single'] == "paired"</filter> - </data> - <data format_source="input" name="output_single" label="${tool.name} on ${on_string}: Normalized reads"> - <filter>inputs['paired_or_single'] == "single"</filter> - </data> - </outputs> - <tests> - <test> - <param name="JM" value="1G"/> - <param name="max_cov" value="30"/> - <param name="paired_or_single" value="single"/> - <param name="input" ftype="fastq" value="reads.left.fq"/> - <param name="library_type" value="None"/> - <output name="trinity_coverage_normalization_log"> - <assert_contents> - <has_text text="Normalization complete." /> - </assert_contents> - </output> - <output name="output_single"> - <assert_contents> - <has_text text="ACTGCATCCTGGAAAGAATCAATGGTGGCCGGAAAGTGTTTTTCAAATACAAGAGTGACAATGTGCCCTGTTGTTT" /> - </assert_contents> - </output> - </test> - <test> - <param name="JM" value="1G"/> - <param name="max_cov" value="30"/> - <param name="paired_or_single" value="paired"/> - <param name="left_input" ftype="fastq" value="reads.left.fq"/> - <param name="right_input" ftype="fastq" value="reads.right.fq"/> - <param name="library_type" value="None"/> - <param name="pe_reads_unordered" value="False"/> - <param name="pairs_together" value="False"/> - <param name="parallel_stats" value="False"/> - <output name="trinity_coverage_normalization_log"> - <assert_contents> - <has_text text="Normalization complete." /> - </assert_contents> - </output> - <output name="output_left"> - <assert_contents> - <has_text text="CTGGGCTGCAGCTAAGTTCTCTGCATCCTCCTTCTTGCTTGTGGCTGGGAAGAAGACAATGTTGTCGATGGTCTGG" /> - </assert_contents> - </output> - <output name="output_right"> - <assert_contents> - <has_text text="CTCAAATGGTTAATTCTCAGGCTGCAAATATTCGTTCAGGATGGAAGAACATTTTCTCAGTATTCCATCTAGCTGC" /> - </assert_contents> - </output> - </test> - </tests> - <help> - Runs script Trinity_ script util/normalize_by_kmer_coverage.pl which reduces data sizes with minimal impact on recovered transcripts when used by Trinity.pl. - - .. _Trinity: http://trinityrnaseq.sourceforge.net - </help> -</tool>