Mercurial > repos > paulgordon > atlas2
changeset 1:da1dba1da40a draft default tip
Uploaded
author | paulgordon |
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date | Mon, 11 Feb 2013 15:43:46 -0500 |
parents | 59d3e3484f16 |
children | |
files | atlas2_indel.xml |
diffstat | 1 files changed, 57 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/atlas2_indel.xml Mon Feb 11 15:43:46 2013 -0500 @@ -0,0 +1,57 @@ +<tool id="atlas2_indel_1" name="Call indels using Atlas2"> + <description></description> + <requirements> + <requirement type="package" version="1.4.1">freebayes</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + <command interpreter="ruby"> + /export/achri_data/programs/Atlas2_v1.4.1/Atlas-Indel2/Atlas-Indel2.rb -b $bam_file -r /export/geno_tmp/achri/dbs/$refgenome\.fa -o $vcf_outfile + -p $max_pvalue -v $min_prop $platform + #if str( $target_limit_type.target_limit_type_selector ) == "limit_by_target_file": + -B "${target_limit_type.input_target_bed}" + #end if + &> /dev/null + </command> + <inputs> + <param name="bam_file" label="Mapped reads file (BAM)" type="data" format="bam" /> + <param name="refgenome" type="genomebuild" label="Reference genome" help="against which indels will be called"/> + <param name="platform" label="Platform used for sequencing" type="select" display="radio"> + <option value="-S" selected="true">SOLiD</option> + <option value="-I">Illumina</option> + </param> + <param name="max_pvalue" label="Maximum p-value to call a variant" type="float" min="0" value="0.01" max="1" help="0.01=~99% random exclusion"/> + <param name="min_prop" label="Minimum proportion of variants to make a call" type="float" min="0.01" value="0.1" max="1.0" /> + <conditional name="target_limit_type"> + <param name="target_limit_type_selector" type="select" label="Limit analysis to listed targets"> + <option value="do_not_limit" selected="True">Do not limit</option> + <option value="limit_by_target_file">Limit by target file</option> + </param> + <when value="do_not_limit"> + <!-- Do nothing here --> + </when> + <when value="limit_by_target_file"> + <param name="input_target_bed" type="data" format="bed" label="Limit analysis to targets listed in the BED-format FILE." /> + </when> + </conditional> + </inputs> + <outputs> + <data name="vcf_outfile" format="vcf" /> + </outputs> + <tests> + <test> + <param name="bam_file" value="test2" /> + <param name="refgenome" value="hg19" /> + <param name="platform" value="-S" /> + <param name="max_pvalue" value="0.01" /> + <param name="min_prop" value="0.1" /> + <output name="vcf_outfile" file="sam_merge_out2.log" ftype="vcf" lines_diff="11"/> + </test> + </tests> + <help> + +**What it does** + +This tools uses the Atlas2 software to call indels in a way that accounts for the systematic error types of either SOLiD or Illumina sequencing. +It does NOT call SNPs. The output is a VCF file, and can be combined with SNP caller output to form a more complete picture of sequence variation. + </help> +</tool>