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author devteam
date Tue, 13 Oct 2015 12:27:32 -0400
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1 <tool id="pgSnp2gd_snp" name="pgSnp to gd_snp" hidden="false" version="1.0.0">
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2 <description>Convert from pgSnp to gd_snp</description>
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3 <command interpreter="perl">
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4 <![CDATA[
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5 #if $snptab.tab2 == "yes"
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6 #if $snptab.needRef.colsOnly == "addColsOnly"
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7 pgSnp2gd_snp.pl '$input1' -tab=${snptab.input2} -name=$indName -build=${input1.metadata.dbkey} -addColsOnly -chr=${input1.metadata.chromCol} > '$out_file1'
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8 #else
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9 pgSnp2gd_snp.pl '$input1' -tab=${snptab.input2} -name=$indName -build=${input1.metadata.dbkey} -ref=${snptab.needRef.ref} -chr=${input1.metadata.chromCol} > '$out_file1'
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10 #end if
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11 #else
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12 pgSnp2gd_snp.pl '$input1' -name=$indName -build=${input1.metadata.dbkey} -ref=${snptab.ref} -chr=${input1.metadata.chromCol} > '$out_file1'
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13 #end if
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param format="tab" name="input1" type="data" label="pgSnp dataset" />
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18 <conditional name="snptab">
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19 <param name="tab2" type="select" label="Append to gd_snp dataset in history">
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20 <option value="yes">yes</option>
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21 <option value="no" selected="true">no</option>
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22 </param>
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23 <when value="yes">
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24 <param format="gd_snp" name="input2" type="data" label="gd_snp dataset" />
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25 <conditional name="needRef">
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26 <param name="colsOnly" type="select" label="Skip new SNPs">
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27 <option value="no" selected="true">no</option>
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28 <option value="addColsOnly">yes</option>
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29 </param>
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30 <when value="no">
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31 <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" />
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32 </when>
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33 <when value="addColsOnly" />
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34 </conditional>
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35 </when>
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36 <when value="no">
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37 <param name="ref" type="data_column" data_ref="input1" label="Column with reference allele" />
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38 </when>
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39 </conditional>
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40 <param name="indName" type="text" label="Label for new individual/group" value="na" />
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41 </inputs>
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42 <outputs>
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43 <data format="gd_snp" name="out_file1" />
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="input1" value="pgSnpTest.ref.txt" ftype="interval" dbkey="hg19" />
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48 <param name="tab2" value="no" />
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49 <param name="ref" value="8" />
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50 <param name="indName" value="na" />
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51 <output name="output" file="pgSnp2snp_output.txt" />
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52 </test>
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53 </tests>
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54
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55 <help>
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56 **Dataset formats**
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57
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58 The input dataset is of Galaxy datatype interval_, with the additional columns
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59 required for pgSnp_ format.
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60 Any further columns beyond those defined for pgSnp will be ignored.
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61 The output dataset is a gd_snp_ table. (`Dataset missing?`_)
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62
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63 .. _interval: ./static/formatHelp.html#interval
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64 .. _pgSnp: ./static/formatHelp.html#pgSnp
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65 .. _gd_snp: ./static/formatHelp.html#gd_snp
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66 .. _Dataset missing?: ./static/formatHelp.html
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67
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68 -----
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69
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70 **What it does**
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71
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72 This tool converts a pgSnp dataset to gd_snp format, either starting a new
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73 dataset or appending to an old one. When appending,
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74 if any new SNPs appear only in the pgSnp file they can either be skipped entirely, or
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75 backfilled with "-1" (meaning "unknown") for previous individuals/groups in the
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76 input gd_snp dataset.
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77 If any new SNPs are being added (either by creating a new table or by backfilling),
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78 then an extra column with the reference allele must be supplied in the pgSnp dataset,
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79 as shown in the example below.
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80
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81 -----
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82
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83 **Example**
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84
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85 - input pgSnp file, with reference allele added::
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86
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87 chr1 1888681 1888682 C/T 2 4,3 0.8893,0.8453 T
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88 chr1 3118325 3118326 T 1 8 0.8796 C
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89 chr1 3211457 3211458 A/C 2 17,10 0.8610,0.8576 A
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90 etc.
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91
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92 - gd_snp output::
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93
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94 chr1 1888681 T C -1 3 4 1 0.8893
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95 chr1 3118325 C T -1 0 8 0 0.8796
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96 chr1 3211457 A C -1 17 10 1 0.8576
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97 etc.
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98 </help>
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99 </tool>