Mercurial > repos > bcrain-completegenomics > testing_cgatools
changeset 5:51fea6716ea5 draft
Deleted selected files
| author | bcrain-completegenomics |
|---|---|
| date | Wed, 13 Jun 2012 17:30:29 -0400 |
| parents | 1fdc01496e71 |
| children | 8a3d71feeb48 |
| files | cgatools/tools/cgatools/join.xml cgatools/tools/cgatools/junctiondiff.xml cgatools/tools/cgatools/listtestvariants.xml cgatools/tools/cgatools/listvariants.xml cgatools/tools/cgatools/snpdiff.xml cgatools/tools/cgatools/testvariants.xml cgatools/tools/cgatools/varfilter.xml cgatools/tools/cgatools/varfilter_wrapper.pl |
| diffstat | 8 files changed, 0 insertions(+), 1353 deletions(-) [+] |
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--- a/cgatools/tools/cgatools/join.xml Wed Jun 13 17:29:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,206 +0,0 @@ -<tool id="cga_join" name="join(beta)" version="0.0.1"> - - <description>two tsv files based on equal fields or overlapping regions.</description> <!--adds description in toolbar--> - - <requirements> - <requirement type="binary">cgatools</requirement> - </requirements> - - <command> <!--run executable--> - cgatools join --beta - --input $inputA - --input $inputB - --output $output - --output-mode $outmode - $dump - --select $col - #for $m in $matches <!--get all matched columns--> - --match ${m.match} - #end for - #if $range_overlap.range == 'yes' - #for $o in $range_overlap.overlaps <!--get all matched columns--> - --overlap ${o.overlap} - #end for - --overlap-mode $range_overlap.overlapmode - --overlap-fraction-A $range_overlap.fractionA - --boundary-uncertainty-A $range_overlap.boundaryA - --overlap-fraction-B $range_overlap.fractionB - --boundary-uncertainty-B $range_overlap.boundaryB - #end if - </command> - - <outputs> - <data format="tabular" name="output" /> - </outputs> - - <inputs> - <!--form field to select input file A--> - <param name="inputA" type="data" format="tabular" label="Select input file A "> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc" - metadata_name="dbkey" metadata_column="0" - message="cgatools is not currently available for this build."/> - </param> - - <!--form field to select input file B--> - <param name="inputB" type="data" format="tabular" label="Select input file B "> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc" - metadata_name="dbkey" metadata_column="0" - message="cgatools is not currently available for this build."/> - </param> - - <!--form field to specify columns to print--> - <param name="col" type="text" value="A.*,B.*" size="40" label="Specify columns for output" help="The default value A.*,B.* prints all columns from both files, other selections enter in the format A.col_name1,A.col_name3,B.col_name1" /> - - <!--form field to select output-mode--> - <param name="outmode" type="select" label="Select output mode"> - <option value="full" selected="true">full (1 line for each match of records in A and B)</option> - <option value="compact">compact (1 line for each record in A, joining multiple records in B by semicolon)</option> - <option value="compact-pct">compact-pct (same as compact, annotated with % overlap)</option> - </param> - - <!--form field to select columns to match--> - <param name="dump" type="select" label="Select records to print"> - <option value="--always-dump" selected="true">print all records of A even if not matched in B</option> - <option value="">print only records of A that are matched in B</option> - </param> - - <!--form field to specify columns to match--> - <repeat name="matches" title="Exact match column"> - <param name="match" type="text" size="40" label="Enter column:column" help="Enter column_from_A:column_from_B, e.g. chromosome:chromosome"/> - </repeat> - - <conditional name="range_overlap"> - <param name="range" type="select" label="Do you want to match columns by overlapping range?"> - <option value="no">no</option> - <option value="yes">yes</option> - </param> - - <when value="yes"> - <!--form field to specify columns to overlap--> - <repeat name="overlaps" title="Range column"> - <param name="overlap" type="text" size="40" label="Enter column[,column]:column[,column]" help="Enter range_start_from_A[,range_stop_from_A]:range_start_from_B[,range_stop_from_B], e.g. begin,end:begin,end (overlapping range of positions) or begin,end:position"/> - </repeat> - - <!--form field to select overlap-mode--> - <param name="overlapmode" type="select" label="Select overlap mode"> - <option value="strict" selected="true">strict (overlap if A.begin<B.end and B.begin>A.end)</option> - <option value="allow-abutting-points">allow-abutting-points (overlap if A.begin<B.end and B.begin>A.end, or if A.begin<=B.end and B.begin<=A.end and either A or B has zero length.)</option> - </param> - - <!--form fields to overlap options--> - <param name="fractionA" type="integer" value="0" label="Minimum fraction of A region overlap " /> - <param name="boundaryA" type="integer" value="0" label="Boundary uncertainty for A for overlap filtering " help="Records failing the following boundary-uncertainty calculation are not included in the output: overlap length >= overlap-fraction-A * (A-range-length - boundary-uncertainty-A)"/> - - <param name="fractionB" type="integer" value="0" label="Minimum fraction of B region overlap " /> - <param name="boundaryB" type="integer" value="0" label="Boundary uncertainty for overlap filtering " help="Records failing the following boundary-uncertainty calculation are not included in the output: overlap length >= overlap-fraction-B * (B-range-length - boundary-uncertainty-B)"/> - </when> - </conditional> - </inputs> - - <help> - -**What it does** - -This tool joins two tab-delimited files based on equal fields or overlapping regions. - -cgatools: http://sourceforge.net/projects/cgatools/files/ - ------ - -**cgatools Manual**:: - - COMMAND NAME - join - Joins two tab-delimited files based on equal fields or overlapping regions. - - DESCRIPTION - Joins two tab-delimited files based on equal fields or overlapping regions. - By default, an output record is produced for each match found between file - A and file B, but output format can be controlled by the --output-mode - parameter. - - OPTIONS - -h [ --help ] - Print this help message. - - --beta - This is a beta command. To run this command, you must pass the --beta - flag. - - --input arg - File name to use as input (may be passed in as arguments at the end of - the command), or omitted for stdin). There must be exactly two input - files to join. If only one file is specified by name, file A is taken - to be stdin and file B is the named file. File B is read fully into - memory, and file A is streamed. File A's columns appear first in the - output. - - --output arg (=STDOUT) - The output file name (may be omitted for stdout). - - --match arg - A match specification, which is a column from A and a column from B - separated by a colon. - - --overlap arg - Overlap specification. An overlap specification consists of a range - definition for files A and B, separated by a colon. A range definition - may be two columns, in which case they are interpreted as the beginning - and end of the range. Or it may be one column, in which case the range - is defined as the 1-base range starting at the given value. The records - from the two files must overlap in order to be considered for output. - Two ranges are considered to overlap if the overlap is at least one - base long, or if one of the ranges is length 0 and the ranges overlap - or abut. For example, "begin,end:offset" will match wherever end-begin - > 0, begin<offset+1, and end>offset, or wherever end-begin = 0, - begin<=offset+1, and end>=offset. - - - -m [ --output-mode ] arg (=full) - Output mode, one of the following: - full Print an output record for each match found between - file A and file B. - compact Print at most one record for each record of file A, - joining the file B values by a semicolon and - suppressing repeated B values and empty B values. - compact-pct Same as compact, but for each distinct B value, - annotate with the percentage of the A record that is - overlapped by B records with that B value. Percentage - is rounded up to nearest integer. - - --overlap-mode arg (=strict) - Overlap mode, one of the following: - strict Range A and B overlap if A.begin < B.end and - B.begin < A.end. - allow-abutting-points Range A and B overlap they meet the strict - requirements, or if A.begin <= B.end and - B.begin <= A.end and either A or B has zero - length. - - --select arg (=A.*,B.*) - Set of fields to select for output. - - -a [ --always-dump ] - Dump every record of A, even if there are no matches with file B. - - --overlap-fraction-A arg (=0) - Minimum fraction of A region overlap for filtering output. - - --boundary-uncertainty-A arg (=0) - Boundary uncertainty for overlap filtering. Specifically, records - failing the following predicate are filtered away: overlap >= - overlap-fraction-A * ( A-range-length - boundary-uncertainty-A ) - - --overlap-fraction-B arg (=0) - Minimum fraction of B region overlap for filtering output. - - --boundary-uncertainty-B arg (=0) - Boundary uncertainty for overlap filtering. Specifically, records - failing the following predicate are filtered away: overlap >= - overlap-fraction-B * ( B-range-length - boundary-uncertainty-B ) - - SUPPORTED FORMAT_VERSION - Any - </help> -</tool>
--- a/cgatools/tools/cgatools/junctiondiff.xml Wed Jun 13 17:29:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,146 +0,0 @@ -<tool id="cga_junctiondiff" name="junctiondiff(beta)" version="0.0.1"> - - <description>reports difference between junction calls</description> <!--adds description in toolbar--> - - <requirements> - <requirement type="binary">cgatools</requirement> - </requirements> - - <command> <!--run executable--> - cgatools junctiondiff --beta - --reference $crr.fields.path - --junctionsA $data_sources.inputA - --junctionsB $data_sources.inputB - --scoreThresholdA $scoreA - --scoreThresholdB $scoreB - --distance $distance - --minlength $minlength - $stat - --output-prefix cg_ - ; - mv cg_diff-*tsv cg_diff.tsv - </command> - - <outputs> - <data format="tabular" name="output1" from_work_dir="cg_diff.tsv" label="${tool.name} on ${on_string}: diff"/> - <data format="tabular" name="output2" from_work_dir="cg_report.tsv" label="${tool.name} on ${on_string}: report"> - <filter>(stat == '--statout')</filter> - </data> - </outputs> - - <inputs> - <!--form field to select crr file--> - <param name="crr" type="select" label="Genome build"> - <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 are the input junction files?"> - <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="inputA" type="data" format="tabluar" label="Junction file A"> - <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="inputB" type="data" format="tabluar" label="Junction file B"> - <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 enter external input files--> - <param name="inputA" type="text" label="Junction file A (path/file_name)" size="40" help="Junction file can be compressed (gz, bz2)."/> - <param name="inputB" type="text" label="Junction file B (path/file_name)" size="40" help="Junction file can be compressed (gz, bz2)."/> - </when> - </conditional> - - <!--form field to select stats output--> - <param name="stat" type="select" label="Print input file stats"> - <option value="">no</option> - <option value="--statout">yes</option> - </param> - - <param name="scoreA" type="integer" label="Score threshold value for input file A (default 10)" value="10"/> - <param name="scoreB" type="integer" label="Score threshold value for input file B (default 0)" value="0"/> - <param name="distance" type="integer" label="Max distance between coordinates of potentially compatible junctions (default 200)" value="200"/> - <param name="minlength" type="integer" label="Minimum deletion junction length to be included into the difference file (default 500)" value="500"/> - </inputs> - - - <help> - -**What it does** - -This tool reports difference between junction calls of Complete Genomics junctions files - -cgatools: http://sourceforge.net/projects/cgatools/files/ - ------ - -**cgatools Manual**:: - - COMMAND NAME - junctiondiff - Reports difference between junction calls of Complete Genomics junctions files. - - DESCRIPTION - junctiondiff takes two junction files A and B as input and produces the - following output: - - "diff-inputFileName" - the junctions from an input file A that are not - present in input file B. - - "report.txt" - a brief summary report (if --statout is used) - - Two junctions are considered equivalent if: - - they come from different files - - left and right positions of one junction are not more than "--distance" - bases apart from the corresponding positions of another junction - - the junction scores are equal or above the scoreThreshold - - they are on the same strands - - OPTIONS - -h [ --help ] - Print this help message. - - --beta - This is a beta command. To run this command, you must pass the --beta - flag. - - -s [ --reference ] arg - Reference file. - - -a [ --junctionsA ] arg - input junction file A. - - -b [ --junctionsB ] arg - input junction file B. - - -A [ --scoreThresholdA ] arg (=10) - score threshold value for the input file A. - - -B [ --scoreThresholdB ] arg (=0) - score threshold value for the input file B. - - -d [ --distance ] arg (=200) - Max distance between coordinates of potentially compatible junctions. - - -l [ --minlength ] arg (=500) - Minimum deletion junction length to be included into the difference - file. - - -o [ --output-prefix ] arg - The path prefix for all the output reports. - - -S [ --statout ] - (Debug) Report various input file statistics. Experimental feature. - - SUPPORTED FORMAT_VERSION - 1.5 or later - </help> -</tool>
--- a/cgatools/tools/cgatools/listtestvariants.xml Wed Jun 13 17:29:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,239 +0,0 @@ -<tool id="cga_listtestvariants" name="listvariants(beta)-testvariants(beta)" version="1.0.1"> -<!-- -This tool creates a GUI for cgatools listvariants and testvariants from Complete Genomics, Inc. -to be run consecutively with the same input files. -written 5-29-2012 by bcrain@completegenomics.com ---> - - <description></description> <!--adds description in toolbar--> - - <requirements> - <requirement type="binary">cgatools</requirement> - </requirements> - - <command> <!--run executable--> - cgatools listvariants - --beta - --reference ${crr.fields.path} - --output $output1 - #if $include_list.listing == "yes" <!--only added when yes--> - --variant-listing $include_list.list - #end if - $longvar - --variants - #if $file_types.data_sources.data_source == "in" - #for $v in $file_types.data_sources.varfiles <!--get each var file--> - ${v.input} - #end for - #else - `cat $file_types.data_sources.varlist` - #end if - ; - - cgatools testvariants - --beta - --reference ${crr.fields.path} - --output $output2 - --input $output1 - --variants - #if $file_types.data_sources.data_source == "in" - #for $v in $file_types.data_sources.varfiles <!--get each var/mastervar file--> - ${v.input} - #end for - #else - `cat $file_types.data_sources.varlist` - #end if - </command> - - <outputs> - <data format="tabular" name="output1" label="listvariants output"/> - <data format="tabular" name="output2" label="testvariants output"/> - </outputs> - - <inputs> - <!--form field to select crr file--> - <param name="crr" type="select" label="Genome build"> - <options from_data_table="cg_crr_files" /> - </param> - - <!--form field to select long variants option--> - <param name="longvar" type="select" label="List long variants?"> - <option value="" selected="true">no</option> - <option value="--list-long-variants">yes</option> - </param> - - <!--form fields to include existing variant list--> - <conditional name="include_list"> - <param name="listing" type="select" label="Include variant listing?"> - <option value="no" selected="true">no</option> - <option value="yes">yes</option> - </param> - <when value="yes"> - <param name="list" type="data" format="tabular" label="Variant listing"> - <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> - </conditional> - - <!--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 are the input var files?"> - <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--> - <repeat name="varfiles" title="Variant files"> - <param name="input" type="data" format="cg_var" label="Dataset"> - <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> - </repeat> - </when> - <when value="out"> - <!--form field to select crr file--> - <param name="varlist" type="text" label="List of variant files (/path/file)" size="200" help="file with list of var files (/path/varfile), var files can be compressed (gz, 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 are the input mastervar files?"> - <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--> - <repeat name="varfiles" title="Variant files"> - <param name="input" type="data" format="cg_mastervar" label="Dataset"> - <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> - </repeat> - </when> - <when value="out"> - <!--form field to select crr file--> - <param name="varlist" type="text" label="List of mastervar files (/path/file)" size="200" help="file with list of mastervar files (/path/varfile), mastervar files can be compressed (gz, bz2)."/> - </when> - </conditional> - </when> - </conditional> - </inputs> - - <help> - -**What it does** - -This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants. - -cgatools: http://sourceforge.net/projects/cgatools/files/ - ------ - -**cgatools Manual**:: - - COMMAND NAME - listvariants - Lists the variants present in a variant file. - - DESCRIPTION - Lists all called variants present in the specified variant files, in a - format suitable for processing by the testvariants command. The output is a - tab-delimited file consisting of the following columns: - - variantId Sequential id assigned to each variant. - chromosome The chromosome of the variant. - begin 0-based reference offset of the beginning of the variant. - end 0-based reference offset of the end of the variant. - varType The varType as extracted from the variant file. - reference The reference sequence. - alleleSeq The variant allele sequence as extracted from the variant - file. - xRef The xRef as extrated from the variant file. - - 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. - - --output arg (=STDOUT) - The output file (may be omitted for stdout). - - --variants arg - The input variant files (may be positional args). - - --variant-listing arg - The output of another listvariants run, to be merged in to produce the - output of this run. - - --list-long-variants - In addition to listing short variants, list longer variants as well - (10's of bases) by concatenating nearby calls. - - SUPPORTED FORMAT_VERSION - 0.3 or later - - - - COMMAND NAME - testvariants - Tests variant files for presence of variants. - - DESCRIPTION - Tests variant files for presence of variants. The output is a tab-delimited - file consisting of the columns of the input variants file, plus a column - for each assembly results file that contains a character code for each - allele. The character codes have meaning as follows: - - 0 This allele of this genome is consistent with the reference at this - locus but inconsistent with the variant. - 1 This allele of this genome has the input variant at this locus. - N This allele of this genome has no-calls but is consistent with the - input variant. - - 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 (=STDIN) - The input variants to test for. - - --output arg (=STDOUT) - The output file (may be omitted for stdout). - - --variants arg - The input variant files (may be passed in as arguments at the end of - the command). - - SUPPORTED FORMAT_VERSION - 0.3 or later - </help> -</tool>
--- a/cgatools/tools/cgatools/listvariants.xml Wed Jun 13 17:29:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,188 +0,0 @@ -<tool id="cga_listvariant" name="listvariants(beta)" version="0.0.1"> -<!-- -This tool creates a GUI for cgatools listvariants from Complete Genomics, Inc. -written 5-29-2012 by bcrain@completegenomics.com ---> - - <description>lists all called variants</description> <!--adds description in toolbar--> - - <requirements> - <requirement type="binary">cgatools</requirement> - </requirements> - - <command> <!--run executable--> - cgatools listvariants - --beta - --reference ${crr.fields.path} - --output $output - #if $include_list.listing == "yes" <!--only added when yes--> - --variant-listing $include_list.list - #end if - $longvar - --variants - #if $file_types.data_sources.data_source == "in" - #for $v in $file_types.data_sources.varfiles <!--get each var/mastervar file--> - ${v.input} - #end for - #else - `cat $file_types.data_sources.varlist` - #end if - </command> - - <inputs> - <!--form field to select crr file--> - <param name="crr" type="select" label="Genome build"> - <options from_data_table="cg_crr_files" /> - </param> - - <!--form field to select long variants option--> - <param name="longvar" type="select" label="List long variants?"> - <option value="" selected="true">no</option> - <option value="--list-long-variants">yes</option> - </param> - - <!--form fields to include existing variant list--> - <conditional name="include_list"> - <param name="listing" type="select" label="Include variant listing?"> - <option value="no" selected="true">no</option> - <option value="yes">yes</option> - </param> - <when value="yes"> - <param name="list" type="data" format="tabular" label="Variant listing"/> - </when> - </conditional> - - <!--conditional to select input file type--> - <conditional name="file_types"> - <param name="file_type" type="select" label="Select the input file type"> - <option value="var" selected="true">var files</option> - <option value="mastervar">mastervar files</option> - </param> - - <when value="var"> - <!--conditional to select variant file input--> - <conditional name="data_sources"> - <param name="data_source" type="select" label="Where are the input var files?"> - <option value="in" selected="true">imported into Galaxy</option> - <option value="out">located outside Galaxy (available only for local Galaxy instances)</option> - </param> - <when value="in"> - <!--form field to select variant files--> - <repeat name="varfiles" title="Variant files"> - <param name="input" type="data" format="cg_var" label="Dataset"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc" - metadata_name="dbkey" metadata_column="1" - message="cgatools is not currently available for this build."/> - <!--<validator type="expression" message="Dataset does not match selected build.">$dbkey == $crr.fields.dbkey</validator>--> - </param> - </repeat> - </when> - <when value="out"> - <!--form field to select crr file--> - <param name="varlist" type="text" label="List of variant files (/path/file)" size="200" help="file with list of var files (/path/varfile), var files can be compressed (gz, 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 are the input mastervar files?"> - <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--> - <repeat name="varfiles" title="Variant files"> - <param name="input" type="data" format="cg_mastervar" label="Dataset"> - <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> - </repeat> - </when> - <when value="out"> - <!--form field to select crr file--> - <param name="varlist" type="text" label="List of mastervar files (/path/file)" size="200" help="file with list of mastervar files (/path/varfile), mastervar files can be compressed (gz, bz2)."/> - </when> - </conditional> - </when> - </conditional> - </inputs> - - <outputs> - <data format="tabular" name="output"/> - </outputs> - -<!-- <tests> - <test> - <param name="reference" value="hg19.crr"/> - <param name="file_type" value="var"/> - <param name="data_source" value="in"/> - <param name="varfiles?input" value="??"/> - <param name="varfiles?input" value="??"/> - <output name="output" file="??"/> - </test> - </tests>--> - - <help> - -**What it does** - -This tool uses the cgatools listvariants to list all called variants present in the var or mastervar files. - -cgatools: http://sourceforge.net/projects/cgatools/files/ - ------ - -**cgatools Manual**:: - - COMMAND NAME - listvariants - Lists the variants present in a variant file. - - DESCRIPTION - Lists all called variants present in the specified variant files, in a - format suitable for processing by the testvariants command. The output is a - tab-delimited file consisting of the following columns: - - variantId Sequential id assigned to each variant. - chromosome The chromosome of the variant. - begin 0-based reference offset of the beginning of the variant. - end 0-based reference offset of the end of the variant. - varType The varType as extracted from the variant file. - reference The reference sequence. - alleleSeq The variant allele sequence as extracted from the variant - file. - xRef The xRef as extrated from the variant file. - - 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. - - --output arg (=STDOUT) - The output file (may be omitted for stdout). - - --variants arg - The input variant files (may be positional args). - - --variant-listing arg - The output of another listvariants run, to be merged in to produce the - output of this run. - - --list-long-variants - In addition to listing short variants, list longer variants as well - (10's of bases) by concatenating nearby calls. - - SUPPORTED FORMAT_VERSION - 0.3 or later - </help> -</tool>
--- a/cgatools/tools/cgatools/snpdiff.xml Wed Jun 13 17:29:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,177 +0,0 @@ -<tool id="cga_snpdiff" name="snpdiff" version="0.0.1"> - - <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 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="Genome build"> - <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/file_name)" size="40" help="Variant file can be compressed (gz, 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="Report Output"> - <option value="">no</option> - <option value="Output">yes</option> - </param> - <param name="report2" type="select" label="Report Verbose"> - <option value="">no</option> - <option value="Verbose">yes</option> - </param> - <param name="report3" type="select" label="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: http://sourceforge.net/projects/cgatools/files/ - ------ - -**cgatools Manual**:: - - 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>
--- a/cgatools/tools/cgatools/testvariants.xml Wed Jun 13 17:29:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,157 +0,0 @@ -<tool id="cga_testvariants" name="testvariants(beta)" version="0.0.1"> -<!-- -This tool creates a GUI for cgatools testvariants from Complete Genomics, Inc. -written 5-29-2012 by bcrain@completegenomics.com ---> - - <description>test for the presence of variants</description> <!--adds description in toolbar--> - - <requirements> - <requirement type="binary">cgatools</requirement> - </requirements> - - <command> <!--run executable--> - cgatools testvariants - --beta - --reference ${crr.fields.path} - --output $output - --input $listing - --variants - #if $file_types.data_sources.data_source == "in" - #for $v in $file_types.data_sources.varfiles <!--get each var/mastervar file--> - ${v.input} - #end for - #else - `cat $file_types.data_sources.varlist` - #end if - </command> - - <outputs> - <data format="tabular" name="output" /> - </outputs> - - <inputs> - <!--form field to select crr file--> - <param name="crr" type="select" label="Genome build"> - <options from_data_table="cg_crr_files" /> - </param> - - <!--form fields to select variant list--> - <param name="listing" type="data" format="tabular" label="Select variant list"> - <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> - - <!--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 are the input var files?"> - <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--> - <repeat name="varfiles" title="Variant files"> - <param name="input" type="data" format="cg_var" label="Dataset"> - <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> - </repeat> - </when> - <when value="out"> - <!--form field to select crr file--> - <param name="varlist" type="text" label="List of variant files (/path/file)" size="200" help="file with list of var files (/path/varfile), var files can be compressed (gz, 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 are the input mastervar files?"> - <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--> - <repeat name="varfiles" title="Variant files"> - <param name="input" type="data" format="cg_mastervar" label="Dataset"> - <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> - </repeat> - </when> - <when value="out"> - <!--form field to select crr file--> - <param name="varlist" type="text" label="List of mastervar files (/path/file)" size="200" help="file with list of mastervar files (/path/varfile), mastervar files can be compressed (gz, bz2)."/> - </when> - </conditional> - </when> - </conditional> - </inputs> - - <help> - -**What it does** - -This tool uses the cgatools testvariants to test variant or mastervar files for the presence of variants. - -cgatools: http://sourceforge.net/projects/cgatools/files/ - ------ - -**cgatools Manual**:: - - COMMAND NAME - testvariants - Tests variant files for presence of variants. - - DESCRIPTION - Tests variant files for presence of variants. The output is a tab-delimited - file consisting of the columns of the input variants file, plus a column - for each assembly results file that contains a character code for each - allele. The character codes have meaning as follows: - - 0 This allele of this genome is consistent with the reference at this - locus but inconsistent with the variant. - 1 This allele of this genome has the input variant at this locus. - N This allele of this genome has no-calls but is consistent with the - input variant. - - 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 (=STDIN) - The input variants to test for. - - --output arg (=STDOUT) - The output file (may be omitted for stdout). - - --variants arg - The input variant files (may be passed in as arguments at the end of - the command). - - SUPPORTED FORMAT_VERSION - 0.3 or later - </help> -</tool>
--- a/cgatools/tools/cgatools/varfilter.xml Wed Jun 13 17:29:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,184 +0,0 @@ -<tool id="cga_varfilter" name="varfilter(beta)" version="0.0.1"> -<!-- -This tool creates a GUI for cgatools varfilter 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 6-1-2012 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"> - 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="Genome build"> - <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="var file can be compressed (gz, 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)."/> - </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: http://sourceforge.net/projects/cgatools/files/ - ------ - -**cgatools Manual**:: - - 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>
--- a/cgatools/tools/cgatools/varfilter_wrapper.pl Wed Jun 13 17:29:06 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -#!/usr/bin/perl -use strict; -use Getopt::Long; -use vars qw($opt_reference $opt_input $opt_output @opt_zygosity @opt_vartype @opt_varscorevaf @opt_varscoreeaf @opt_varquality); -$| = 1; # set autoflush to screen - -# This is a wrapper for the cgatools varfilter function to run cgatools varfilter in Galaxy. -# The wrapper generates the filter(s) in the correct format to be used with the input file. -# written 6-1-2012 by bcrain@completegenomics.com - - -#print join("\n", @ARGV), "\n"; -&GetOptions("reference=s", "input=s", "output=s", "zygosity=s@", "vartype=s@", "varscorevaf=s@", "varscoreeaf=s@", "varquality=s@"); - -my $append = ''; - -for (my $i = 0; $i <= $#opt_zygosity; $i ++) -{ - my $filter = ''; - unless ($opt_zygosity[$i] eq 'NA') {$filter = $opt_zygosity[$i];} - unless ($opt_vartype[$i] eq 'NA') - { - $filter ne '' and $filter .= ':'; - $filter .= 'varType=' . $opt_vartype[$i]; - } - unless ($opt_varscorevaf[$i] eq 'x') - { - $filter ne '' and $filter .= ':'; - $opt_varscorevaf[$i] =~ s/^x//; - $filter .= 'varScoreVAF<' . $opt_varscorevaf[$i]; - } - unless ($opt_varscoreeaf[$i] eq 'x') - { - $filter ne '' and $filter .= ':'; - $opt_varscoreeaf[$i] =~ s/^x//; - $filter .= 'varScoreEAF<' . $opt_varscoreeaf[$i]; - } - unless ($opt_varquality[$i] eq 'NA') - { - $filter ne '' and $filter .= ':'; - $filter .= 'varQuality!=' . $opt_varquality[$i]; - } - - if ($filter ne '') - { - if ($append eq '') {$append = '#' . $filter;} - else {$append .= ',' . $filter;} - } -} -print "cgatools varfilter ---beta ---reference $opt_reference ---output $opt_output ---input '${opt_input}${append}'\n"; - -`cgatools varfilter --beta --reference $opt_reference --output $opt_output --input '${opt_input}${append}'`; \ No newline at end of file