Mercurial > repos > iuc > gemini_dump

annotate gemini_dump.xml @ 4:96a2d270bf0f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
author iuc
date Fri, 14 Dec 2018 12:58:00 -0500
parents a32c298053e4
children
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rev   line source
4
96a2d270bf0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
0
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2 <description>Extract data from the Gemini DB</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">dump</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
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12 gemini @BINARY@
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13 $report
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14 $header
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15 $tfam
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16
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17 "${ infile }"
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18 > "${ outfile }"
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19 ]]>
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20 </command>
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21 <inputs>
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22 <expand macro="infile" />
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23
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24 <param name="report" type="select" label="The information to be reported" help="(-t)">
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25 <option value="--variants">All rows/columns from the variants table (--variants)</option>
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26 <option value="--genotypes">All rows/columns from the variants table with one line per sample/genotype (--genotypes)</option>
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27 <option value="--samples">All rows/columns from the samples table (--samples)</option>
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28 </param>
2
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29 <param argument="--header" type="boolean" label="Include a header of column names" truevalue="--header" falsevalue="" checked="False" />
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30 <param argument="--tfam" type="boolean" label="Output sample information to TFAM information" truevalue="--tfam" falsevalue="" checked="False" />
0
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31 </inputs>
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32 <outputs>
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33 <data name="outfile" format="tabular" />
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34 </outputs>
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35 <tests>
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36 <test>
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37 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
0
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38 <param name="header" value="True" />
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39 <param name="report" value="--genotypes" />
4
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40 <output name="outfile">
96a2d270bf0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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41 <assert_contents>
96a2d270bf0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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42 <has_line_matching expression="chrom&#009;start&#009;end&#009;.*sample&#009;.*genotype.*" />
96a2d270bf0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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43 </assert_contents>
96a2d270bf0f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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44 </output>
0
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45 </test>
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46 </tests>
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47 <help><![CDATA[
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48 **What it does**
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49
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50 Reports information in a Gemini database.
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51
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52 **Setting examples**
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53
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54
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55 **--samples**
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56
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57 GEMINI output with setting --samples (and --header)::
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58
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59 sample_id family_id name paternal_id maternal_id sex phenotype
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60 1 1 1_dad 0 0 -1 1
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61 2 1 1_mom 0 0 -1 1
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62 3 1 1_kid 1_dad 1_mom -1 2
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63 4 2 2_dad 0 0 -1 1
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64 5 2 2_mom 0 0 -1 2
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65 6 2 2_kid 2_dad 2_mom -1 2
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66 7 3 3_dad 0 0 -1 2
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67 8 3 3_mom 0 0 -1 -9
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68 9 3 3_kid 3_dad 3_mom -1 2
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69
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70
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71 **--variants**
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72
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73 GEMINI output with setting --variants (and --header)::
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74
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75 chrom start end vcf_id variant_id anno_id ref alt qual filter type sub_type ...
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76 chr10 1142207 1142208 . 1 4 T C 3404.30004883 . snp ts ...
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77 chr10 48003991 48003992 . 3 1 C T 1047.86999512 . snp ts ...
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78
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79
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80 **--genotypes**
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81
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82 GEMINI output with setting --genotypes (and --header)::
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83
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84 chrom start end ref alt type sub_type aaf in_dbsnp gene sample genotype
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85 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 1_dad T/T
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86 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 1_mom T/T
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87 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 1_kid T/C
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88 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 2_dad T/T
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parents:
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89 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 2_mom T/C
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
90 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 2_kid T/C
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
91 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 3_dad T/C
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
92 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 3_mom T/T
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
93 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 3_kid T/C
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
94 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 1_dad C/C
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
95 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 1_mom C/C
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
96 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 1_kid C/T
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
97 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 2_dad C/C
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
98 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 2_mom C/T
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
99 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 2_kid C/T
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
100 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 3_dad C/T
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
101 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 3_mom C/C
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
102 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 3_kid C/T
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
103 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 1_dad C/C
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
104 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 1_mom C/C
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
105 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 1_kid C/T
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
106 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 2_dad C/C
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
107 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 2_mom C/T
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
108 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 2_kid C/T
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
109
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
110
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
111 ]]></help>
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
112 <expand macro="citations"/>
187b57debbba planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
diff changeset
113 </tool>