Mercurial > repos > wolma > mimodd
changeset 5:bdd1995c9e66
upgrade to mimodd version 0.1.6.1
author | Wolfgang Maier |
---|---|
date | Tue, 28 Jul 2015 23:21:11 +0200 (2015-07-28) |
parents | ffee8534a5c4 |
children | 85214e4428fd |
files | annotate_variants.xml bamsort.xml cloudmap.xml convert.xml covstats.xml deletion_predictor.xml fileinfo.xml reheader.xml sam_header.xml snap_caller.xml snp_caller_caller.xml snpeff_genomes.xml tool_dependencies.xml toolshed_macros.xml varextract.xml vcf_filter.xml |
diffstat | 16 files changed, 41 insertions(+), 23 deletions(-) [+] |
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--- a/annotate_variants.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/annotate_variants.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,4 +1,4 @@ -<tool id="annotate_variants" name="Variant Annotation"> +<tool id="annotate_variants" name="Variant Annotation" version="0.1.6.1"> <description>Predict the effects of SNPs and indels on known genes in the reference genome using SnpEff</description> <macros> <import>toolshed_macros.xml</import>
--- a/bamsort.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/bamsort.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,4 +1,4 @@ -<tool id="bamsort" name="Sort BAM file"> +<tool id="bamsort" name="Sort BAM file" version="0.1.6.1"> <description>Sort a BAM file by coordinates (or names) of the mapped reads</description> <macros> <import>toolshed_macros.xml</import> @@ -6,13 +6,27 @@ <expand macro="requirements"/> <version_command>mimodd version -q</version_command> <command> - mimodd sort "$inputfile" -o "$output" --oformat $oformat $by_name + mimodd sort "$input.ifile" -o "$output" --iformat $input.iformat --oformat $oformat $by_name </command> <inputs> - <param name="inputfile" type="data" format="bam" label="Input file to sort" /> + <conditional name="input"> + <param name="iformat" type="select" label = "Input data format"> + <option value="bam">bam</option> + <option value="sam">sam</option> + </param> + <when value="bam"> + <param name="ifile" type="data" format="bam" label="BAM input file to sort" /> + </when> + <when value="sam"> + <param name="ifile" type="data" format="sam" label="SAM input file to sort" /> + </when> + </conditional> + <param name="oformat" type="select" label = "Output format for the sorted data"> + <option value="bam">bam</option> + <option value="sam">sam</option> + </param> <param name="by_name" type="boolean" truevalue = "-n" falsevalue ="" label="Sort by read names instead of coordinates" checked = "false" help="A less common option, but necessary, e.g., if you want to re-align sorted output from a previous run of the Snap Align Tool." /> - <param name="oformat" type="boolean" truevalue = "sam" falsevalue = "bam" label = "Output in uncompressed SAM format" checked = "false" /> </inputs> <outputs>
--- a/cloudmap.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/cloudmap.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,4 +1,4 @@ -<tool id="cloudmap_prepare" name="Prepare variant data for mapping"> +<tool id="cloudmap_prepare" name="Prepare variant data for mapping" version="0.1.6.1"> <description>with the CloudMap series of tools.</description> <macros> <import>toolshed_macros.xml</import>
--- a/convert.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/convert.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,4 +1,4 @@ -<tool id="convert" name="Convert"> +<tool id="convert" name="Convert" version="0.1.6.1"> <description>between different sequence data formats</description> <macros> <import>toolshed_macros.xml</import>
--- a/covstats.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/covstats.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,4 +1,4 @@ -<tool id="coverage_stats" name="Coverage Statistics"> +<tool id="coverage_stats" name="Coverage Statistics" version="0.1.6.1"> <description>Calculate coverage statistics for a BCF file as generated by the Variant Calling tool</description> <macros> <import>toolshed_macros.xml</import>
--- a/deletion_predictor.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/deletion_predictor.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,4 +1,4 @@ -<tool id="deletion_prediction" name="Deletion Prediction for paired-end data"> +<tool id="deletion_prediction" name="Deletion Prediction for paired-end data" version="0.1.6.1"> <description>Predicts deletions in one or more aligned read samples based on coverage of the reference genome and on insert sizes</description> <macros> <import>toolshed_macros.xml</import>
--- a/fileinfo.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/fileinfo.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,4 +1,4 @@ -<tool id="fileinfo" name="Retrieve File Information"> +<tool id="fileinfo" name="Retrieve File Information" version="0.1.6.1"> <description>for supported data formats.</description> <macros> <import>toolshed_macros.xml</import>
--- a/reheader.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/reheader.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,5 +1,4 @@ -<tool id="reheader" name="Reheader BAM file"> - +<tool id="reheader" name="Reheader BAM file" version="0.1.6.1"> <description>From a BAM file generate a new file with the original header (if any) replaced or modified by that found in a second SAM file</description> <expand macro="requirements"/> <version_command>mimodd version -q</version_command> @@ -83,7 +82,7 @@ #set $restr = "" #for $rename in $rg_renaming - #set $restr = $restr + ($str($rename.from) and $str($rename.to) and '"' + $str($rename.from) + '" : "' + $str($rename.to) + '"') + #set $restr = $restr + ($str($rename.from) and $str($rename.to) and '"' + $str($rename.from) + '" : "' + $str($rename.to) + '" ') #end for #if $restr --rgm $restr @@ -91,7 +90,7 @@ #set $restr = "" #for $rename in $sq_renaming - #set $restr = $restr + ($str($rename.from) and $str($rename.to) and '"' + $str($rename.from) + '" : "' + $str($rename.to) + '"') + #set $restr = $restr + ($str($rename.from) and $str($rename.to) and '"' + $str($rename.from) + '" : "' + $str($rename.to) + '" ') #end for #if $restr --sqm $restr
--- a/sam_header.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/sam_header.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,4 +1,4 @@ -<tool id="ngs_run_annotation" name="NGS Run Annotation"> +<tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.6.1"> <description>Create a SAM format header from run metadata for sample annotation.</description> <macros> <import>toolshed_macros.xml</import>
--- a/snap_caller.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/snap_caller.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,4 +1,4 @@ -<tool id="read_alignment" name="SNAP Read Alignment"> +<tool id="read_alignment" name="SNAP Read Alignment" version="0.1.6.1"> <description>Map sequence reads to a reference genome using SNAP</description> <macros> <import>toolshed_macros.xml</import>
--- a/snp_caller_caller.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/snp_caller_caller.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,4 +1,4 @@ -<tool id="variant_calling" name="Variant Calling"> +<tool id="variant_calling" name="Variant Calling" version="0.1.6.1"> <description>From a reference and aligned reads generate a BCF file with position-specific variant likelihoods and coverage information</description> <macros> <import>toolshed_macros.xml</import>
--- a/snpeff_genomes.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/snpeff_genomes.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,4 +1,4 @@ -<tool id="snpeff_genomes" name="List Installed SnpEff Genomes"> +<tool id="snpeff_genomes" name="List Installed SnpEff Genomes" version="0.1.6.1"> <description>Checks the local SnpEff installation to compile a list of currently installed genomes</description> <macros> <import>toolshed_macros.xml</import>
--- a/tool_dependencies.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/tool_dependencies.xml Tue Jul 28 23:21:11 2015 +0200 @@ -7,10 +7,10 @@ <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="mimodd" version="0.1.6"> + <package name="mimodd" version="0.1.6.1"> <install version="1.0"> <actions> - <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.6.tar.gz</action> + <action type="download_by_url">http://sourceforge.net/projects/mimodd/files/MiModD-0.1.6.1.tar.gz</action> <action type="set_environment_for_install"> <repository changeset_revision="1c337560fa56" name="package_python3_zlib_dependent_1_0" owner="wolma" toolshed="https://toolshed.g2.bx.psu.edu"> <package name="python3" version="3.4.1" />
--- a/toolshed_macros.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/toolshed_macros.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,7 +1,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="0.1.6">mimodd</requirement> + <requirement type="package" version="0.1.6.1">mimodd</requirement> </requirements> </xml> </macros>
--- a/varextract.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/varextract.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,4 +1,4 @@ -<tool id="extract_variants" name="Extract Variant Sites"> +<tool id="extract_variants" name="Extract Variant Sites" version="0.1.6.1"> <description>from a BCF file</description> <macros> <import>toolshed_macros.xml</import>
--- a/vcf_filter.xml Thu Jun 04 17:52:04 2015 +0200 +++ b/vcf_filter.xml Tue Jul 28 23:21:11 2015 +0200 @@ -1,4 +1,4 @@ -<tool id="vcf_filter" name="VCF Filter"> +<tool id="vcf_filter" name="VCF Filter" version="0.1.6.1"> <description>Extracts lines from a vcf variant file based on field-specific filters</description> <macros> <import>toolshed_macros.xml</import> @@ -28,6 +28,10 @@ #for $i in $datasets "$i.GQ" #end for + --af + #for $i in $datasets + "#echo ($i.AF or "::")#" + #end for #end if #if len($regions): -r @@ -54,6 +58,7 @@ <param name="GT" type="text" label="genotype pattern(s) for the inclusion of variants" help="keep only variants for which the genotype of the sample matches the specified pattern; format: x/x where x = 0 is wildtype and x = 1 is mutant. Multiple genotypes can be specified as a comma-separated list." /> <param name="DP" type="integer" label="depth of coverage for the sample at the variant site" value = "0" help="keep only variants with at least this sample-specific coverage at the variant site" /> <param name="GQ" type="integer" label="genotype quality for the variant in the sample" value = "0" help="keep only variants for which the genotype prediction for the sample has at least this quality" /> + <param name="AF" type="text" label="allelic fraction filter" help="expected format: [allele number]:[minimal fraction]:[maximal fraction]; keep only variants for which the fraction of sample-specific reads supporting a given allele number is between minimal and maximal fraction; if allele number is omitted, the filter operates on the most frequent non-reference allele instead" /> </repeat> <repeat name="regions" title="Region Filter" default="0" min="0" help = "Filter variant sites by their position in the genome. If multiple Region Filters are specified, all variants that fall in ONE of the regions are reported."> <param name="chrom" type="text" label="Chromosome" />