Mercurial > repos > miller-lab > snp_analysis_conversion

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