Mercurial > repos > miller-lab > snp_analysis_conversion

annotate master2pg.xml @ 2:35c20b109be5

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