Mercurial > repos > iuc > gemini_dump

annotate gemini_dump.xml @ 4:7b24461e6bc3 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 85a2af25c79df4758afe9f846e11ef0af16b1c1f
author iuc
date Mon, 17 Dec 2018 12:21:48 -0500
parents a48f00c341dc
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
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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 $tfam
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17 "${ 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 <!-- The genotypes option is broken in gemini v0.20.1.
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27 Add this option back in once there is an upstream fix!
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28 Remember then to replace all underscores with dashes on the following line. They are only there to not break this comment!
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29 <option value="__genotypes">All rows/columns from the variants table with one line per sample/genotype (__genotypes)</option>
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30 -->
0
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31 <option value="--samples">All rows/columns from the samples table (--samples)</option>
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32 </param>
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33 <param argument="--header" type="boolean" label="Include a header of column names" truevalue="--header" falsevalue="" checked="False" />
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34 <param argument="--tfam" type="boolean" label="Output sample information to TFAM information" truevalue="--tfam" falsevalue="" checked="False" />
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35 </inputs>
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36 <outputs>
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37 <data name="outfile" format="tabular" />
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38 </outputs>
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39 <tests>
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40 <test>
4
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41 <param name="infile" value="gemini_de_novo_input.db" ftype="gemini.sqlite" />
0
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42 <param name="header" value="True" />
4
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43 <param name="report" value="--samples" />
3
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44 <output name="outfile">
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45 <assert_contents>
4
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46 <has_line_matching expression="sample_id&#009;family_id&#009;name&#009;paternal_id&#009;maternal_id&#009;sex&#009;phenotype" />
3
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47 </assert_contents>
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48 </output>
0
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52 **What it does**
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53
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54 Reports information in a Gemini database.
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55
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56 **Setting examples**
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57
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58
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59 **--samples**
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61 GEMINI output with setting --samples (and --header)::
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63 sample_id family_id name paternal_id maternal_id sex phenotype
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64 1 1 1_dad 0 0 -1 1
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65 2 1 1_mom 0 0 -1 1
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66 3 1 1_kid 1_dad 1_mom -1 2
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67 4 2 2_dad 0 0 -1 1
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68 5 2 2_mom 0 0 -1 2
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69 6 2 2_kid 2_dad 2_mom -1 2
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70 7 3 3_dad 0 0 -1 2
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71 8 3 3_mom 0 0 -1 -9
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72 9 3 3_kid 3_dad 3_mom -1 2
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75 **--variants**
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77 GEMINI output with setting --variants (and --header)::
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79 chrom start end vcf_id variant_id anno_id ref alt qual filter type sub_type ...
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80 chr10 1142207 1142208 . 1 4 T C 3404.30004883 . snp ts ...
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81 chr10 48003991 48003992 . 3 1 C T 1047.86999512 . snp ts ...
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84 **--genotypes**
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86 GEMINI output with setting --genotypes (and --header)::
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87
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88 chrom start end ref alt type sub_type aaf in_dbsnp gene sample genotype
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89 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 1_dad T/T
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90 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 1_mom T/T
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
91 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 1_kid T/C
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
92 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 2_dad T/T
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
93 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 2_mom T/C
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
94 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 2_kid T/C
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
95 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 3_dad T/C
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
96 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 3_mom T/T
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
97 chr10 1142207 1142208 T C snp ts 0.277777777778 1 WDR37 3_kid T/C
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
98 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 1_dad C/C
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
99 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 1_mom C/C
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
100 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 1_kid C/T
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
101 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 2_dad C/C
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
102 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 2_mom C/T
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
103 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 2_kid C/T
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
104 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 3_dad C/T
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
105 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 3_mom C/C
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
106 chr10 48003991 48003992 C T snp ts 0.277777777778 1 ASAH2C 3_kid C/T
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
107 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 1_dad C/C
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
108 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 1_mom C/C
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
109 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 1_kid C/T
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
110 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 2_dad C/C
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
111 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 2_mom C/T
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
diff changeset
112 chr10 48004991 48004992 C T snp ts 0.277777777778 0 ASAH2C 2_kid C/T
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
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113
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
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114
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
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115 ]]></help>
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
parents:
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116 <expand macro="citations"/>
65845dad49e7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 2f3c5976d08f63f05e1d9726343d03a478dc035b-dirty
iuc
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117 </tool>