Mercurial > repos > miller-lab > snp_analysis_conversion

annotate pgSnp2gd_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="pgSnp2gd_snp" name="pgSnp to gd_snp" version="1.1.0" hidden="false">
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2 <description>: Convert from pgSnp 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.needRef.colsOnly == "addColsOnly" #pgSnp2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -addColsOnly -chr=${input1.metadata.chromCol} > $out_file1
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6 #else #pgSnp2gd_snp.pl $input1 -tab=$snptab.input2 -name=$indName -build=${input1.metadata.dbkey} -ref=${snptab.needRef.ref} -chr=${input1.metadata.chromCol} > $out_file1
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7 #end if
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8 #else #pgSnp2gd_snp.pl $input1 -name=$indName -build=${input1.metadata.dbkey} -ref=${snptab.ref} -chr=${input1.metadata.chromCol} > $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="interval" name="input1" type="data" label="pgSnp 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 <conditional name="needRef">
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21 <param name="colsOnly" type="select" label="Skip new SNPs">
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22 <option value="no" selected="true">no</option>
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23 <option value="addColsOnly">yes</option>
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24 </param>
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25 <when value="no">
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26 <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" />
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27 </when>
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28 <when value="addColsOnly"> <!-- do nothing -->
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29 </when>
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30 </conditional>
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31 </when>
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32 <when value="no">
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33 <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" />
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34 </when>
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35 </conditional>
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36 <param name="indName" type="text" size="20" label="Label for new individual/group" value="na" />
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37 </inputs>
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38 <outputs>
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39 <data format="gd_snp" name="out_file1" />
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40 </outputs>
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41 <tests>
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42 <test>
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43 <param name='input1' value='pgSnpTest.ref.txt' ftype='interval' />
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44 <param name='tab2' value='no' />
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45 <param name='ref' value='8' />
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46 <param name='indName' value='na' />
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47 <output name="output" file="pgSnp2snp_output.txt" />
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48 </test>
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49 </tests>
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50
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51 <help>
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52
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53 **Dataset formats**
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54
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55 The input dataset is of Galaxy datatype interval_, with the additional columns
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56 required for pgSnp_ format.
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57 Any further columns beyond those defined for pgSnp will be ignored.
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58 The output dataset is in gd_snp_ format. (`Dataset missing?`_)
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59
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60 .. _interval: ./static/formatHelp.html#interval
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61 .. _pgSnp: ./static/formatHelp.html#pgSnp
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62 .. _gd_snp: ./static/formatHelp.html#gd_snp
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63 .. _Dataset missing?: ./static/formatHelp.html
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64
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65 -----
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66
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67 **What it does**
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68
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69 This tool converts a pgSnp dataset to gd_snp format, either starting a new
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70 dataset or appending to an old one. When appending,
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71 if any new SNPs appear only in the pgSnp file they can either be skipped entirely, or
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72 backfilled with "-1" (meaning "unknown") for previous individuals/groups in the
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73 input gd_snp dataset.
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74 If any new SNPs are being added (either by creating a new dataset or by backfilling),
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75 then an extra column with the reference allele must be supplied in the pgSnp dataset,
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76 as shown in the example below.
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77
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78 -----
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79
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80 **Example**
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81
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82 - input pgSnp file, with reference allele added::
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83
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84 chr1 1888681 1888682 C/T 2 4,3 0.8893,0.8453 T
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85 chr1 3118325 3118326 T 1 8 0.8796 C
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86 chr1 3211457 3211458 A/C 2 17,10 0.8610,0.8576 A
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87 etc.
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88
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89 - gd_snp output::
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90
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91 chr1 1888681 T C -1 3 4 1 0.8893
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92 chr1 3118325 C T -1 0 8 0 0.8796
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93 chr1 3211457 A C -1 17 10 1 0.8576
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94 etc.
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95
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96 </help>
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97 </tool>