Mercurial > repos > bcrain-completegenomics > testing1
diff cgatools_suite/tools/cgatools/junctiondiff.xml @ 7:96829b1b73ea draft
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author | bcrain-completegenomics |
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date | Wed, 06 Jun 2012 16:58:26 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cgatools_suite/tools/cgatools/junctiondiff.xml Wed Jun 06 16:58:26 2012 -0400 @@ -0,0 +1,88 @@ +<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 -h + </command> + + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <inputs> + </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>