Mercurial > repos > miller-lab > snp_analysis_conversion
comparison master2gd_snp.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 |
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| children |
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| 1:1d8b23a21735 | 2:35c20b109be5 |
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| 1 <tool id="master2gd_snp" name="MasterVar to gd_snp" version="1.1.0" hidden="false"> | |
| 2 <description>: Convert from MasterVar to gd_snp format</description> | |
| 3 <command interpreter="perl"> | |
| 4 #if $snptab.tab2 == "yes" | |
| 5 #if $snptab.colsOnly.value == "addColsOnly" #master2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -addColsOnly > $out_file1 | |
| 6 #else #master2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} > $out_file1 | |
| 7 #end if | |
| 8 #else #master2gd_snp.pl $input1 -name=$indName -build=${input1.metadata.dbkey} > $out_file1 | |
| 9 #end if | |
| 10 </command> | |
| 11 <inputs> | |
| 12 <param format="tabular" name="input1" type="data" label="Complete Genomics MasterVar dataset" /> | |
| 13 <conditional name="snptab"> | |
| 14 <param name="tab2" type="select" label="Append to gd_snp dataset in history"> | |
| 15 <option value="yes">yes</option> | |
| 16 <option value="no" selected="true">no</option> | |
| 17 </param> | |
| 18 <when value="yes"> | |
| 19 <param format="gd_snp" name="input2" type="data" label="gd_snp dataset" /> | |
| 20 <param name="colsOnly" type="select" label="Skip new SNPs"> | |
| 21 <option value="" selected="true">no</option> | |
| 22 <option value="addColsOnly">yes</option> | |
| 23 </param> | |
| 24 </when> | |
| 25 <when value="no"> <!-- do nothing --> | |
| 26 </when> | |
| 27 </conditional> | |
| 28 <param name="indName" type="text" size="20" label="Label for new individual/group" value="na" /> | |
| 29 </inputs> | |
| 30 <outputs> | |
| 31 <data format="gd_snp" name="out_file1" /> | |
| 32 </outputs> | |
| 33 <tests> | |
| 34 <test> | |
| 35 <param name='input1' value='masterVarTest.txt' ftype='tab' /> | |
| 36 <param name='tab2' value='no' /> | |
| 37 <param name='indName' value='na' /> | |
| 38 <output name="output" file="master2snp_output.txt" /> | |
| 39 </test> | |
| 40 </tests> | |
| 41 | |
| 42 <help> | |
| 43 | |
| 44 **Dataset formats** | |
| 45 | |
| 46 The input dataset is in the MasterVar_ format provided by the Complete Genomics | |
| 47 analysis process (Galaxy considers this to be tabular_, but it must have the | |
| 48 columns specified for MasterVar). | |
| 49 The output dataset is in gd_snp_ format. (`Dataset missing?`_) | |
| 50 | |
| 51 .. _MasterVar: ./static/formatHelp.html#mastervar | |
| 52 .. _tabular: ./static/formatHelp.html#tab | |
| 53 .. _gd_snp: ./static/formatHelp.html#gd_snp | |
| 54 .. _Dataset missing?: ./static/formatHelp.html | |
| 55 | |
| 56 ----- | |
| 57 | |
| 58 **What it does** | |
| 59 | |
| 60 This converts a Complete Genomics MasterVar file to gd_snp format, | |
| 61 so it can be used with the Genome Diversity tools. It can either | |
| 62 start a new dataset or append to an old one. When appending, if any new SNPs | |
| 63 appear only in the MasterVar file they can either be skipped or backfilled with | |
| 64 "-1" (unknown) for previous individuals/groups in the gd_snp dataset. | |
| 65 Positions homozygous for the reference allele are skipped. | |
| 66 | |
| 67 ----- | |
| 68 | |
| 69 **Example** | |
| 70 | |
| 71 - input MasterVar file:: | |
| 72 | |
| 73 934 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 | |
| 74 935 2 chr1 41981 42198 hom ref = = = -170 1.17 N | |
| 75 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 | |
| 76 etc. | |
| 77 | |
| 78 - output:: | |
| 79 | |
| 80 chr1 41980 A G -1 0 1 0 76 | |
| 81 chr1 53205 G C -1 30 7 1 93 | |
| 82 etc. | |
| 83 | |
| 84 </help> | |
| 85 </tool> |