Mercurial > repos > miller-lab > snp_analysis_conversion
comparison master2pg.xml @ 2:35c20b109be5
Retrying upload with "bare" tarball (i.e. one without a top containing directory).
| author | cathy |
|---|---|
| date | Tue, 28 May 2013 17:54:02 -0400 |
| parents | |
| children |
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| 1:1d8b23a21735 | 2:35c20b109be5 |
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| 1 <tool id="master2pgSnp" name="MasterVar to pgSnp" version="1.1.0" hidden="false"> | |
| 2 <description>: Convert from MasterVar to pgSnp format</description> | |
| 3 <command interpreter="perl"> | |
| 4 master2pg.pl $indel $addRef $input1 > $out_file1 | |
| 5 </command> | |
| 6 <inputs> | |
| 7 <param format="tabular" name="input1" type="data" label="Complete Genomics MasterVar dataset" /> | |
| 8 <param name="indel" type="select" label="Convert indels"> | |
| 9 <option value="" selected="true">no</option> | |
| 10 <option value="indel">yes</option> | |
| 11 </param> | |
| 12 <param name="addRef" type="select" label="Add column with reference nt"> | |
| 13 <option value="" selected="true">no</option> | |
| 14 <option value="addRef">yes</option> | |
| 15 </param> | |
| 16 </inputs> | |
| 17 <outputs> | |
| 18 <data format="interval" name="out_file1" /> | |
| 19 </outputs> | |
| 20 <tests> | |
| 21 <test> | |
| 22 <param name='input1' value='masterVarTest.txt' ftype='tab' /> | |
| 23 <param name='indel' value="" /> | |
| 24 <output name="output" file="masterVar_output.txt" /> | |
| 25 </test> | |
| 26 </tests> | |
| 27 | |
| 28 <help> | |
| 29 | |
| 30 **Dataset formats** | |
| 31 | |
| 32 The input dataset is in the MasterVar_ format provided by the Complete Genomics | |
| 33 analysis process (Galaxy considers this to be tabular_, but it must have the | |
| 34 columns specified for MasterVar). | |
| 35 The output dataset is in pgSnp_ format. (`Dataset missing?`_) | |
| 36 | |
| 37 .. _MasterVar: ./static/formatHelp.html#mastervar | |
| 38 .. _tabular: ./static/formatHelp.html#tab | |
| 39 .. _pgSnp: ./static/formatHelp.html#pgSnp | |
| 40 .. _Dataset missing?: ./static/formatHelp.html | |
| 41 | |
| 42 ----- | |
| 43 | |
| 44 **What it does** | |
| 45 | |
| 46 This converts a Complete Genomics MasterVar file to pgSnp format, | |
| 47 so it can be viewed in genome browsers or used with the Phenotype Association | |
| 48 and Operate on Genomic Intervals tools. | |
| 49 Positions homozygous for the reference allele are skipped. | |
| 50 You can optionally add the reference nt as an extra column at the end. This | |
| 51 will make the file not work in genome browsers (the extra column could be | |
| 52 removed later) but will work with other Galaxy tools. | |
| 53 | |
| 54 ----- | |
| 55 | |
| 56 **Example** | |
| 57 | |
| 58 - input MasterVar file:: | |
| 59 | |
| 60 934 2 chr1 41980 41981 hom snp A G G 76 97 dbsnp.86:rs806721 425 1 1 1 2 -170 ERVL-E-int:ERVL:47.4 2 1.17 N | |
| 61 935 2 chr1 41981 42198 hom ref = = = -170 1.17 N | |
| 62 1102 2 chr1 53205 53206 het-ref snp G C G 93 127 dbsnp.100:rs2854676 477 7 30 0 37 -127 2 1.17 N | |
| 63 etc. | |
| 64 | |
| 65 - output:: | |
| 66 | |
| 67 chr1 41980 41981 G 1 1 76 | |
| 68 chr1 51672 51673 C 1 1 53 | |
| 69 chr1 52237 52238 G 1 7 63 | |
| 70 chr1 53205 53206 C/G 2 7,30 93,127 | |
| 71 etc. | |
| 72 | |
| 73 </help> | |
| 74 </tool> |