Mercurial > repos > saskia-hiltemann > cgatools_v17
comparison tools/cgatools17/junctiondiff_v17.xml @ 1:3a2e0f376f26 draft
Minor change to tv2vcf.xml to allow for workflow automation
| author | dgdekoning |
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| date | Wed, 21 Oct 2015 10:09:15 -0400 |
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| 0:751b62d30ae1 | 1:3a2e0f376f26 |
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| 1 <tool id="cg_junctiondiff" name="JunctionDiff" version="1.7.1"> | |
| 2 | |
| 3 <description>Reports difference between junction calls</description> <!--adds description in toolbar--> | |
| 4 | |
| 5 <requirements> | |
| 6 <requirement type="package" version="1">cgatools17</requirement> | |
| 7 </requirements> | |
| 8 | |
| 9 <command > <!--run executable--> | |
| 10 cgatools | head -1; | |
| 11 cgatools junctiondiff --beta | |
| 12 --reference ${crr.fields.crr_path} | |
| 13 --junctionsA $inputA | |
| 14 --junctionsB $inputB | |
| 15 --scoreThresholdA $scoreA | |
| 16 --scoreThresholdB $scoreB | |
| 17 --distance $distance | |
| 18 --minlength $minlength | |
| 19 $stat | |
| 20 --output-prefix cg_ | |
| 21 ; | |
| 22 mv cg_diff-* cg_diff.tsv | |
| 23 </command> | |
| 24 | |
| 25 <inputs> | |
| 26 <!-- reference --> | |
| 27 <param name="crr" type="select" label="Reference Build"> | |
| 28 <options from_data_table="cg_anno_files" /> | |
| 29 </param> | |
| 30 | |
| 31 <!--input files--> | |
| 32 <param name="inputA" type="data" format="tabluar" label="Junction file A"/> | |
| 33 <param name="inputB" type="data" format="tabluar" label="Junction file B"/> | |
| 34 | |
| 35 <!--parameters--> | |
| 36 <param name="stat" type="select" label="Print input file stats"> | |
| 37 <option value="">no</option> | |
| 38 <option value="--statout">yes</option> | |
| 39 </param> | |
| 40 | |
| 41 <param name="scoreA" type="integer" label="Score threshold value for input file A (default 10)" value="10"/> | |
| 42 <param name="scoreB" type="integer" label="Score threshold value for input file B (default 0)" value="0"/> | |
| 43 <param name="distance" type="integer" label="Max distance between coordinates of potentially compatible junctions (default 200)" value="200"/> | |
| 44 <param name="minlength" type="integer" label="Minimum deletion junction length to be included into the difference file (default 500)" value="500"/> | |
| 45 | |
| 46 <!-- prefix for output file so you dont have to manually rename history items --> | |
| 47 <param name="fname" type="text" value="" label="Prefix for your output file" help="Optional"/> | |
| 48 </inputs> | |
| 49 | |
| 50 <outputs> | |
| 51 <data format="tabular" name="corrected_junctions" from_work_dir="cg_diff.tsv" label="$fname ${tool.name} on ${on_string}: diff"/> | |
| 52 <data format="tabular" name="report" from_work_dir="cg_report.tsv" label="$fname ${tool.name} on ${on_string}: report"> | |
| 53 <filter>(stat == '--statout')</filter> | |
| 54 </data> | |
| 55 </outputs> | |
| 56 | |
| 57 | |
| 58 <help> | |
| 59 **What it does** | |
| 60 | |
| 61 This tool reports difference between junction calls of Complete Genomics junctions files | |
| 62 | |
| 63 **cgatools 1.7.1 Documentation** | |
| 64 | |
| 65 Userguide: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-user-guide.pdf | |
| 66 | |
| 67 Release notes: http://cgatools.sourceforge.net/docs/1.7.1/cgatools-release-notes.pdf | |
| 68 | |
| 69 **Command line reference**:: | |
| 70 | |
| 71 COMMAND NAME | |
| 72 junctiondiff - Reports difference between junction calls of Complete Genomics junctions files. | |
| 73 | |
| 74 DESCRIPTION | |
| 75 junctiondiff takes two junction files A and B as input and produces the | |
| 76 following output: | |
| 77 - "diff-inputFileName" - the junctions from an input file A that are not | |
| 78 present in input file B. | |
| 79 - "report.txt" - a brief summary report (if --statout is used) | |
| 80 | |
| 81 Two junctions are considered equivalent if: | |
| 82 - they come from different files | |
| 83 - left and right positions of one junction are not more than "--distance" | |
| 84 bases apart from the corresponding positions of another junction | |
| 85 - the junction scores are equal or above the scoreThreshold | |
| 86 - they are on the same strands | |
| 87 | |
| 88 OPTIONS | |
| 89 -h [ --help ] | |
| 90 Print this help message. | |
| 91 | |
| 92 --beta | |
| 93 This is a beta command. To run this command, you must pass the --beta | |
| 94 flag. | |
| 95 | |
| 96 -s [ --reference ] arg | |
| 97 Reference file. | |
| 98 | |
| 99 -a [ --junctionsA ] arg | |
| 100 input junction file A. | |
| 101 | |
| 102 -b [ --junctionsB ] arg | |
| 103 input junction file B. | |
| 104 | |
| 105 -A [ --scoreThresholdA ] arg (=10) | |
| 106 score threshold value for the input file A. | |
| 107 | |
| 108 -B [ --scoreThresholdB ] arg (=0) | |
| 109 score threshold value for the input file B. | |
| 110 | |
| 111 -d [ --distance ] arg (=200) | |
| 112 Max distance between coordinates of potentially compatible junctions. | |
| 113 | |
| 114 -l [ --minlength ] arg (=500) | |
| 115 Minimum deletion junction length to be included into the difference | |
| 116 file. | |
| 117 | |
| 118 -o [ --output-prefix ] arg | |
| 119 The path prefix for all the output reports. | |
| 120 | |
| 121 -S [ --statout ] | |
| 122 (Debug) Report various input file statistics. Experimental feature. | |
| 123 | |
| 124 SUPPORTED FORMAT_VERSION | |
| 125 1.5 or later | |
| 126 </help> | |
| 127 </tool> |