Mercurial > repos > iuc > gemini_db_info

annotate gemini_db_info.xml @ 2:124c5faef773 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 11ee7ac206d41894c0b6a11f2439aaea490824f0
author iuc
date Thu, 09 Nov 2017 13:14:19 -0500
parents dc56b2d9d27c
children f3cc64057b4e
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dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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2 <description>List the gemini database tables and columns</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@">db_info</token>
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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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" />
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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10 <command>
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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11 <![CDATA[
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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12 gemini @BINARY@
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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13 "${ infile }" | tr -s ' ' '\t'
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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14 > "${ outfile }"
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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15 ]]>
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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16 </command>
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17 <inputs>
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18 <expand macro="infile" />
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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19 </inputs>
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20 <outputs>
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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21 <data name="outfile" format="tabular" />
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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22 </outputs>
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23 <tests>
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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24 <test>
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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25 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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26 <output name="outfile" file="gemini_dbinfo_result.tabular" />
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27 </test>
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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28 </tests>
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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29 <help><![CDATA[
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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30 **What it does**
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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31
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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32 Because of the sheer number of annotations that are stored in gemini, there are admittedly too many columns to remember by rote.
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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33 If you can’t recall the name of particular column, just use the db_info tool.
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34 It will report all of the tables and all of the columns / types in each table::
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35
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36 table_name column_name type
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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37 variants chrom text
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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38 variants start integer
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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39 variants end integer
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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40 variants variant_id integer
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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41 variants anno_id integer
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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42 variants ref text
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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43 variants alt text
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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44 variants qual float
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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45 variants filter text
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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46 variants type text
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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47 variants sub_type text
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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48 variants gts blob
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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49 variants gt_types blob
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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50 variants gt_phases blob
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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51 variants gt_depths blob
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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52 variants call_rate float
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iuc
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53 variants in_dbsnp bool
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54 variants rs_ids text
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55 variants in_omim bool
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56 variants clin_sigs text
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57 variants cyto_band text
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58 variants rmsk text
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59 variants in_cpg_island bool
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60 variants in_segdup bool
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61 variants is_conserved bool
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62 variants num_hom_ref integer
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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63 variants num_het integer
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64 variants num_hom_alt integer
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65 variants num_unknown integer
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66 variants aaf float
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67 variants hwe float
dc56b2d9d27c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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68 variants inbreeding_coeff float
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69 variants pi float
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70 variants recomb_rate float
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71 variants gene text
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72 variants transcript text
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73 variants is_exonic bool
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74 variants is_coding bool
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75 variants is_lof bool
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76 variants exon text
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77 variants codon_change text
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78 variants aa_change text
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79 ... ... ...
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80
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81 For more columns see https://gemini.readthedocs.org/en/latest/content/tools.html#db-info-list-the-gemini-database-tables-and-columns
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82
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83 ]]></help>
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84 <expand macro="citations"/>
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85 </tool>