Mercurial > repos > completegenomics > cg_cgatools_linux
diff cgatools/tools/cgatools_1.5/snpdiff.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/snpdiff.xml Mon Jun 18 20:15:00 2012 -0400 @@ -0,0 +1,184 @@ +<tool id="cg_snpdiff" name="snpdiff 1.5" version="1.0.0"> +<!-- +This tool creates a GUI for the snpdiff function of cgatools from Complete Genomics, Inc. +written 6-18-2012 by bcrain@completegenomics.com +--> + + <description>compares snp calls to a Complete Genomics variant file.</description> <!--adds description in toolbar--> + + <requirements> + <requirement type="binary">cgatools</requirement> + </requirements> + + <command> <!--run executable--> + cgatools | head -1; + cgatools snpdiff + --reference $crr.fields.path + --variants $varfile + --genotypes $genotype + --output-prefix cg_ + --reports `echo ${report1} ${report2} ${report3} | sed 's/ */,/g'` + </command> + + <outputs> + <data format="tabular" name="output1" from_work_dir="cg_Output.tsv" label="${tool.name} on ${on_string}: Output"> + <filter>(report1 == 'Output')</filter> + </data> + <data format="tabular" name="output2" from_work_dir="cg_Verbose.tsv" label="${tool.name} on ${on_string}: Verbose"> + <filter>(report2 == 'Verbose')</filter> + </data> + <data format="tabular" name="output3" from_work_dir="cg_Stats.tsv" label="${tool.name} on ${on_string}: Stats"> + <filter>(report3 == 'Stats')</filter> + </data> + </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 variant file input--> + <conditional name="data_sources"> + <param name="data_source" type="select" label="Where is the input varfile?"> + <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="varfile" 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="varfile" type="text" label="Variant file (/path/varfile)" size="40" 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> + + <!--conditional to select genotypes file input--> + <param name="genotype" type="data" format="tabular" label="Genotypes file with SNP calls" help="The genotypes file is a tab-delimited file with at + least the following columns (additional columns may be given): Chromosome (Required), Offset0Based (Required), GenotypesStrand (Optional), Genotypes (Optional)"> + <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> + + <param name="report1" type="select" label="Create report Output"> + <option value="">no</option> + <option value="Output">yes</option> + </param> + <param name="report2" type="select" label="Create report Verbose"> + <option value="">no</option> + <option value="Verbose">yes</option> + </param> + <param name="report3" type="select" label="Create report Stats"> + <option value="">no</option> + <option value="Stats">yes</option> + </param> + + </inputs> + + <help> + +**What it does** + +This tool ompares snp calls to a Complete Genomics variant file. + +**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 + snpdiff - Compares snp calls to a Complete Genomics variant file. + + DESCRIPTION + Compares the snp calls in the "genotypes" file to the calls in a Complete + Genomics variant file. The genotypes file is a tab-delimited file with at + least the following columns (additional columns may be given): + + Chromosome (Required) The name of the chromosome. + Offset0Based (Required) The 0-based offset in the chromosome. + GenotypesStrand (Optional) The strand of the calls in the Genotypes + column (+ or -, defaults to +). + Genotypes (Optional) The calls, one per allele. The following + calls are recognized: + A,C,G,T A called base. + N A no-call. + - A deleted base. + . A non-snp variation. + + The output is a tab-delimited file consisting of the columns of the + original genotypes file, plus the following additional columns: + + Reference The reference base at the given position. + VariantFile The calls made by the variant file, one per allele. + The character codes are the same as is described for + the Genotypes column. + DiscordantAlleles (Only if Genotypes is present) The number of + Genotypes alleles that are discordant with calls in + the VariantFile. If the VariantFile is described as + haploid at the given position but the Genotypes is + diploid, then each genotype allele is compared + against the haploid call of the VariantFile. + NoCallAlleles (Only if Genotypes is present) The number of + Genotypes alleles that were no-called by the + VariantFile. If the VariantFile is described as + haploid at the given position but the Genotypes is + diploid, then a VariantFile no-call is counted twice. + + The verbose output is a tab-delimited file consisting of the columns of the + original genotypes file, plus the following additional columns: + + Reference The reference base at the given position. + VariantFile The call made by the variant file for one allele (there is + a line in this file for each allele). The character codes + are the same as is described for the Genotypes column. + [CALLS] The rest of the columns are pasted in from the VariantFile, + describing the variant file line used to make the call. + + The stats output is a comma-separated file with several tables describing + the results of the snp comparison, for each diploid genotype. The tables + all describe the comparison result (column headers) versus the genotype + classification (row labels) in different ways. The "Locus classification" + tables have the most detailed match classifications, while the "Locus + concordance" tables roll these match classifications up into "discordance" + and "no-call". A locus is considered discordant if it is discordant for + either allele. A locus is considered no-call if it is concordant for both + alleles but has a no-call on either allele. The "Allele concordance" + describes the comparison result on a per-allele basis. + + OPTIONS + -h [ --help ] + Print this help message. + + --reference arg + The input crr file. + + --variants arg + The input variant file. + + --genotypes arg + The input genotypes file. + + --output-prefix arg + The path prefix for all output reports. + + --reports arg (=Output,Verbose,Stats) + Comma-separated list of reports to generate. A report is one of: + Output The output genotypes file. + Verbose The verbose output file. + Stats The stats output file. + + SUPPORTED FORMAT_VERSION + 0.3 or later + </help> +</tool>