Mercurial > repos > iuc > gemini_stats

annotate gemini_macros.xml @ 8:b92cfa44f5be draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 15:31:49 +0000
parents 86d4303cc3ca
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
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1 <macros>
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cdd90678004a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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2 <!-- gemini version to be used -->
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86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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3 <token name="@VERSION@">0.20.1</token>
4
cdd90678004a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
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4 <!-- minimal annotation files version required by this version of gemini -->
5
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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5 <token name="@DB_VERSION@">200</token>
4
cdd90678004a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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6
8
b92cfa44f5be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
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7 <xml name="bio_tools">
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8 <xrefs>
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9 <xref type="bio.tools">gemini</xref>
b92cfa44f5be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
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10 </xrefs>
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11 </xml>
b92cfa44f5be planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
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12
0
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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13 <xml name="requirements">
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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14 <requirements>
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cdd90678004a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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15 <requirement type="package" version="@VERSION@">gemini</requirement>
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ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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16 <yield />
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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17 </requirements>
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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18 </xml>
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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20 <xml name="version_command">
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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21 <version_command>gemini --version</version_command>
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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22 </xml>
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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24 <xml name="stdio">
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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25 <stdio>
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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26 <exit_code range="1:" />
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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27 <exit_code range=":-1" />
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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28 <regex match="Error:" />
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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29 <regex match="Exception:" />
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30 <yield />
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31 </stdio>
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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32 </xml>
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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33
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34 <xml name="citations">
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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35 <citations>
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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36 <citation type="doi">10.1371/journal.pcbi.1003153</citation>
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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37 <yield />
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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38 </citations>
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
iuc
parents: 4
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39 </xml>
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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40
0
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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41 <xml name="annotation_dir">
4
cdd90678004a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
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42 <param name="annotation_databases" type="select" label="Choose a gemini annotation source">
cdd90678004a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
iuc
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43 <options from_data_table="gemini_versioned_databases">
0
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44 <filter type="sort_by" column="0" />
4
cdd90678004a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 283362494058ed64143b1f27afb447b8a1cb4313
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45 <filter type="static_value" column="2" value="@DB_VERSION@" />
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ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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46 </options>
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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47 </param>
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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48 </xml>
ac761838cdaf planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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49
5
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50 <xml name="infile">
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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51 <param name="infile" type="data" format="gemini.sqlite" label="GEMINI database" help="Only files with version @VERSION@ are accepted." >
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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52 <options options_filter_attribute="metadata.gemini_version" >
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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53 <filter type="add_value" value="@VERSION@" />
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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54 </options>
0
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55 </param>
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56 </xml>
5
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57
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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58 <xml name="add_header_column">
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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59 <param argument="--header" name="header" type="boolean" truevalue="--header" falsevalue="" checked="True"
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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60 label="Add a header of column names to the output" />
0
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61 </xml>
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62
5
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63 <xml name="column_filter" token_help="" token_minimalset="variant_id, gene">
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64 <conditional name="report">
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65 <param name="report_selector" type="select"
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66 label="Set of columns to include in the variant report table"
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67 help="@HELP@">
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68 <option value="minimal">Minimal (report only a preconfigured minimal set of columns)</option>
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69 <option value="full">Full (report all columns defined in the GEMINI database variants table)</option>
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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70 <option value="custom">Custom (report user-specified columns)</option>
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71 </param>
5
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72 <when value="full" />
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73 <when value="minimal">
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74 <param name="columns" type="hidden" value="@MINIMALSET@" />
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75 <param name="extra_cols" type="hidden" value="" />
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76 </when>
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77 <when value="custom">
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78 <param name="columns" type="select" display="checkboxes" multiple="true" optional="true"
86d4303cc3ca planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit 62ed732cba355e695181924a8ed4cce49ca21c59
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79 label="Choose columns to include in the report" help="(--columns)">
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80 <option value="gene">gene</option>
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81 <option value="chrom">chrom</option>
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82 <option value="start">start</option>
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83 <option value="end">end</option>
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84 <option value="ref">ref</option>
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85 <option value="alt">alt</option>
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86 <option value="impact">impact</option>
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87 <option value="impact_severity">impact_severity</option>
5
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88 <option value="max_aaf_all">alternative allele frequency (max_aaf_all)</option>
0
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89 </param>
5
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90 <param name="extra_cols" type="text"
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91 label="Additional columns (comma-separated)"
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92 help="Column must be specified by the exact name they have in the GEMINI database, e.g., is_exonic or num_hom_alt, but, for genotype columns, GEMINI wildcard syntax is supported. The order of columns in the list is maintained in the output.">
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93 <expand macro="sanitize_query" />
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94 </param>
0
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95 </when>
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96 </conditional>
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97 </xml>
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98
5
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99 <xml name="filter" token_argument="--filter">
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100 <param argument="@ARGUMENT@" name="filter" type="text"
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101 label="Additional constraints expressed in SQL syntax"
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102 help="Constraints defined here will become the WHERE clause of the SQL query issued to the GEMINI database. E.g. alt='G' or impact_severity = 'HIGH'.">
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103 <expand macro="sanitize_query" />
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104 </param>
0
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105 </xml>
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106
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107 <xml name="sanitize_query">
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108 <sanitizer invalid_char="">
3
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109 <valid initial="string.printable">
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110 <remove value="&apos;" />
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111 </valid>
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112 <mapping initial="none">
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113 <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
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114 </mapping>
0
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115 </sanitizer>
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116 </xml>
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117
5
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118 <xml name="lenient" token_argument="--lenient" token_truevalue="--lenient" token_help="The exact consequence of this setting depends on the type of inheritance pattern you are looking for (see the tool help below).">
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119 <param argument="@ARGUMENT@" name="lenient" type="boolean" truevalue="@TRUEVALUE@" falsevalue="" checked="False"
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120 label="Include hits with less convincing inheritance patterns"
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121 help= "@HELP@" />
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122 </xml>
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123
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124 <xml name="unaffected">
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125 <param argument="--allow-unaffected" name="allow_unaffected" type="boolean" truevalue="--allow-unaffected" falsevalue="" checked="False"
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126 label="Report candidates shared by unaffected samples"
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127 help="Activating this option will enable the reporting of variants as candidate causative even if they are shared by unaffected samples in the family tree. The default will only report variants that are unique to affected samples."/>
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128 </xml>
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129
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130 <xml name="min_kindreds" token_label="Minimum number of families with a candidate variant for a gene to be reported" token_help="This is the number of families required to have a variant fitting the inheritance model in the same gene in order for the gene and its variants to be reported. For example, we may only be interested in candidates where at least 4 families have a variant (with a fitting inheritance pattern) in that gene.">
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131 <param argument="--min-kindreds" name="min_kindreds" type="integer" value="1" min="1"
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132 label="@LABEL@"
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133 help="@HELP@" />
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134 </xml>
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135
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136 <xml name="insert_constraint" token_max_repeat="1">
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137 <repeat name="constraint" title="Additional constraints on variants" default="0" max="@MAX_REPEAT@">
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138 <expand macro="filter" />
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139 <yield />
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140 </repeat>
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141 </xml>
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142
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143 <xml name="overwritable_where_default" token_default_where="">
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144 <param name="overwrite_default_filter" type="boolean" checked="false"
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145 label="Overwrite the default constraint of this tool"
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146 help="By default, this tool restricts its analysis to @DEFAULT_WHERE@ and this constraint is applied on top of any constraint expressed above. With this option here selected, your custom constraint, if given, will overwrite the default instead." />
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147 </xml>
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148
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149 <xml name="gt_filter" token_default_repeat="0" token_min_repeat="0" token_max_repeat="1">
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150 <repeat name="filter_by_genotype" title="Genotype filter expression" default="@DEFAULT_REPEAT@" min="@MIN_REPEAT@" max="@MAX_REPEAT@">
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151 <param argument="--gt-filter" name="gt_filter" type="text" value="" area="True" size="5x50"
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152 label="Restrictions to apply to genotype values" help="">
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153 <expand macro="sanitize_query" />
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154 <validator type="expression" message="Genotype filter expression cannot be empty">value.strip()</validator>
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155 </param>
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156 <yield />
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157 </repeat>
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158 </xml>
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159
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160 <xml name="sample_filter">
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161 <repeat name="filter_by_sample" title="Sample filter expression" default="0" max="1">
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162 <param argument="--sample-filter" name="sample_filter" type="text" area="True" size="5x50"
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163 label="SQL filter to use to filter the sample table" help="">
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164 <expand macro="sanitize_query" />
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165 <validator type="expression" message="Sample filter expression cannot be empty">value.strip()</validator>
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166 </param>
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167 <param argument="--in" name="in" type="select"
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168 label="A variant must be in either all, none or any samples passing the sample-query filter"
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169 help="">
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170 <option value="">Return a variant if it is found in any sample passing the sample filter. (default) </option>
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171 <option value="--in all">Return a variant if it is found in ALL samples passing the sample filter. (all)</option>
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172 <option value="--in none">Return a variant if it is found in NO sample passing the sample filter. (none)</option>
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173 <option value="--in only">Return a variant if it is found in any sample passing the sample filter, and in NO sample NOT passing it. (only)</option>
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174 <option value="--in only all">Return a variant if is found in ALL samples passing the sample filter, and in NO sample NOT passing it. (only all)</option>
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175 </param>
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176 <expand macro="min_kindreds"
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177 label="Minimum number of families in which a variant must pass the sample filter" help=""/>
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178 <param argument="--family-wise" name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False"
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179 label="Apply the sample-filter on a family-wise basis" help="If a variant passes the sample filter in at least the minimum number of families specified above it is retained." />
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180 </repeat>
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181 </xml>
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182
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183 <xml name="region_filter">
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184 <repeat name="regions" title="Region Filter" default="0" min="0"
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185 help="Filter variant sites by their position in the genome. If multiple Region Filters are specified, all variants that fall in ONE of the regions are reported.">
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186 <param name="chrom" type="text" label="Chromosome">
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187 <validator type="regex" message="A chromosome identifier is required when specifying a region filter. It should start with 'chr'">^chr[0-9a-zA-Z: _.-]+</validator>
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188 </param>
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189 <param name="start" type="text" label="Region Start">
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190 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
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191 </param>
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192 <param name="stop" type="text" label="Region End">
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193 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
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194 </param>
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195 </repeat>
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196 </xml>
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197
4
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198 <token name="@PROVIDE_ANNO_DATA@"><![CDATA[
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199 mkdir gemini &&
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200 ln -s '${annotation_databases.fields.path}/gemini/data' gemini/data &&
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201 export GEMINI_CONFIG='${annotation_databases.fields.path}' &&
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202 ]]></token>
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203
3
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204 <token name="@MULTILN_SQL_EXPR_TO_CMDLN@">
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205 #set $sql_expr = str($multiline_sql_expr).strip()
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206 #if str($sql_expr):
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207 #set $sql_expr = $sql_expr.replace('\r\n', '\n')
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208 #set $sql_expr = $sql_expr.replace('\r', '\n')
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209 #set $sql_expr = $sql_expr.replace('\\\n', ' ')
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210 $cmdln_param '$sql_expr'
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211 #end if
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212 </token>
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213
5
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214 <token name="@SET_COLS@">
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215 #if str($report.report_selector) == 'full':
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216 #set cols = "*"
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217 #else:
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218 #if $report.columns and str($report.columns) != '':
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219 #set $cols = str($report.columns)
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220 #else
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221 #set $cols = ''
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222 #end if
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223 #if str($report.extra_cols).strip():
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224 #if $cols:
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225 #set $cols = $cols + ', ' + str($report.extra_cols)
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226 #else:
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227 #set $cols = str($report.extra_cols)
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228 #end if
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229 #end if
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230 #if not $cols:
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231 #set $cols = "variant_id, gene"
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232 #end if
0
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233 #end if
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234 </token>
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235
2
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236 <token name="@COLUMN_SELECT@">
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237 @SET_COLS@
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238 #if $cols != "*"
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239 --columns '$cols'
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240 #end if
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241 </token>
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242
5
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243 <token name="@PARSE_REGION_ELEMENTS@"><![CDATA[
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244 #set $region_elements = []
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245 #for $r in $regions:
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246 ## The actual chromosome name needs to be single-quoted
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247 ## in SQL, so we need to quote the single quotes like the
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248 ## sanitize_query macro would if the whole was a parameter.
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249 #set $r_elements = ["chrom = '\"'\"'%s'\"'\"'" % str($r.chrom).strip()]
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250 #if str($r.start).strip():
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251 #silent $r_elements.append("start >= %d" % int($r.start))
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252 #end if
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253 #if str($r.stop).strip():
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254 #silent $r_elements.append("end <= %d" % int($r.stop))
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255 #end if
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256 #silent $region_elements.append("(%s)" % " AND ".join($r_elements))
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257 #end for
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258 ]]>
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259 </token>
0
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260 </macros>