Mercurial > repos > completegenomics > cg_cgatools_linux
diff cgatools/tools/cgatools_1.5/varfilter.xml @ 0:182426b32995 draft default tip
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| author | completegenomics |
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| date | Mon, 18 Jun 2012 20:15:00 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cgatools/tools/cgatools_1.5/varfilter.xml Mon Jun 18 20:15:00 2012 -0400 @@ -0,0 +1,187 @@ +<tool id="cg_varfilter" name="varfilter(beta) 1.5" version="1.0.0"> +<!-- +This tool creates a GUI for the varfilter function of cgatools from Complete Genomics, Inc. +The function is called via a Perl script vartools_wrapper.pl, designed to generate the correctly formated filters to append the input file on the command line. +written 6-18-2012 by bcrain@completegenomics.com +--> + + <description>copies input file, applying filters.</description> <!--adds description in toolbar--> + + <requirements> + <requirement type="binary">cgatools</requirement> + </requirements> + + <command interpreter="perl"> + cgatools | head -1; + varfilter_wrapper.pl + --reference $crr.fields.path + --output $output + --input $file_types.data_sources.input + #for $f in $filters + --zygosity $f.zygosity + --vartype $f.vartype + --varscorevaf x$f.varscorevaf + --varscoreeaf x$f.varscoreeaf + --varquality $f.varquality + #end for + </command> + + <outputs> + <data format="cg_var" name="output" /> + </outputs> + + <inputs> + <!--form field to select crr file--> + <param name="crr" type="select" label="Reference genome (.crr file)"> + <options from_data_table="cg_crr_files" /> + </param> + + <!--conditional to select input file type--> + <conditional name="file_types"> + <param name="file_type" type="select" label="Select the input file type"> + <option value="var" selected="true">var files</option> + <option value="mastervar">mastervar files</option> + </param> + + <when value="var"> + <!--conditional to select variant file input--> + <conditional name="data_sources"> + <param name="data_source" type="select" label="Where is the input var file?"> + <option value="in" selected="true">imported into Galaxy</option> + <option value="out">located outside Galaxy (available only for local Galaxy instances)</option> + </param> + <when value="in"> + <!--form field to select variant files--> + <param name="input" type="data" format="cg_var" label="Var file"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc" + metadata_name="dbkey" metadata_column="1" + message="cgatools is not currently available for this build."/> + </param> + </when> + <when value="out"> + <!--form field to select crr file--> + <param name="input" type="text" label="Var file (/path/file)" size="200" help="Variant file can be compressed (gz, bz2), e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/var-GS00000YYYY-ASM.tsv.bz2"/> + </when> + </conditional> + </when> + + <when value="mastervar"> + <!--conditional to select variant file input--> + <conditional name="data_sources"> + <param name="data_source" type="select" label="Where is the input mastervar file?"> + <option value="in" selected="true">imported into Galaxy</option> + <option value="out">located outside Galaxy (available only for local Galaxy instances)</option> + </param> + <when value="in"> + <!--form field to select variant files--> + <param name="input" type="data" format="cg_mastervar" label="Mastervar file"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc" + metadata_name="dbkey" metadata_column="1" + message="cgatools is not currently available for this build."/> + </param> + </when> + <when value="out"> + <!--form field to select crr file--> + <param name="input" type="text" label="Mastervar file (/path/file)" size="200" help="Mastervar file can be compressed (gz, bz2), e.g. /harddrive/GS00000XXXX-DID/GS00000YYYY-ASM/GS00123-DNA_G01_2000/ASM/masterVarBeta-GS00000YYYY-ASM.tsv.bz2"/> + </when> + </conditional> + </when> + </conditional> + + <!-- formfields to add filters --> + <repeat name="filters" title="Filter"> + <param name="zygosity" type="select" label="Filter out call (set to no-call) IF locus IS"> + <option value="NA">- all loci -</option> + <option value="hom">homozygous</option> + <option value="het">heterzygous</option> + </param> + + <param name="vartype" type="select" label="AND varType IS"> + <option value="NA">- any varType -</option> + <option value="snp">snp</option> + <option value="ins">ins</option> + <option value="del">del</option> + <option value="sub">sub</option> + <option value="ref">ref</option> + </param> + + <param name="varscorevaf" type="text" label="AND varScoreVAF IS LESS THAN"/> + <param name="varscoreeaf" type="text" label="AND varScoreEAF IS LESS THAN"/> + + <param name="varquality" type="select" label="AND varQuality IS NOT"> + <option value="NA"> </option> + <option value="VQHigh">VQHigh</option> + <option value="VQLOW">VQLOW</option> + </param> + </repeat> + </inputs> + + <help> + +**What it does** + +This tool copies input var file or masterVar file to output, applying specified filters. + +**cgatools 1.5.0 Documentation** + +Userguide: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-user-guide.pdf + +Release notes: http://cgatools.sourceforge.net/docs/1.5.0/cgatools-release-notes.pdf + +**Command line reference**:: + + COMMAND NAME + varfilter - Copies input var file or masterVar file to output, applying + specified filters. + + DESCRIPTION + Copies input var file or masterVar file to output, applying specified + filters (which are available to all cgatools commands that read a var file + or masterVar file as input). Filters are specified by appending the filter + specification to the var file name on the command line. For example: + + /path/to/var.tsv.bz2#varQuality!=VQHIGH + + The preceding example filters out any calls marked as VQLOW. The filter + specification follows the "#" sign, and consists of a list of filters to + apply, separated by a comma. Each filter is a colon-separated list of call + selectors. Any scored call that passes all the colon-separated call + selectors for one or more of the comma-separated filters is turned into a + no-call. The following call selectors are available: + + hom Selects only calls in homozygous loci. + het Selects any scored call not selected by the hom selector. + varType=XX Selects calls whose varType is XX. + varScoreVAF<XX Selects calls whose varScoreVAF<XX. + varScoreEAF<XX Selects calls whose varScoreEAF<XX. + varQuality!=XX Selects calls whose varQuality is not XX. + + Here is an example that filters homozygous SNPs with varScoreVAF < 25 and + heterozygous insertions with varScoreEAF < 50: + + + '/path/to/var.tsv.bz2#hom:varType=snp:varScoreVAF<25,het:varType=ins:varScoreEAF<50' + + + OPTIONS + -h [ --help ] + Print this help message. + + --beta + This is a beta command. To run this command, you must pass the --beta flag. + + --reference arg + The reference crr file. + + --input arg + The input var file or masterVar file (typically with filters specified). + + --output arg (=STDOUT) + The output file (may be omitted for stdout). + + SUPPORTED FORMAT_VERSION + 0.3 or later + </help> +</tool>