Mercurial > repos > iuc > gemini_interactions

annotate gemini_interactions.xml @ 4:a6d326ffbb72 draft

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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 12:50:32 -0500
parents 527c8e4a356f
children 7028ca3cac1c
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4
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.1">
0
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2 <description>Find genes among variants that are interacting partners</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@">interactions</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[
4
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12 @PROVIDE_ANNO_DATA@
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13
0
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14 gemini
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15 #if $gene.gene_selector == 'lof':
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16 ## lof interactions is a separate program
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17 lof_interactions
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18 #else:
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19 ## use normal gemini interactions program
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20 @BINARY@
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21 -g "${gene.gene}"
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22 #end if
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23
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24 -r "${radius}"
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25 $variant_mode
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26 "${ infile }"
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27 > "${ outfile }"
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28 ]]>
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29 </command>
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30 <inputs>
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31 <expand macro="infile" />
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32
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33 <conditional name="gene">
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34 <param name="gene_selector" type="select" label="Studying" help="">
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35 <option value="gene">Interesting gene</option>
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36 <option value="lof">All loss-of-function variants</option>
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37 </param>
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38 <when value="gene">
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39 <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (-g)" />
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40 </when>
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41 <when value="lof"/>
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42 </conditional>
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43 <expand macro="annotation_dir" />
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44 <expand macro="radius" />
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45 <expand macro="variant_mode" />
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46 </inputs>
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47 <outputs>
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48 <data name="outfile" format="tabular" />
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49 </outputs>
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50 <tests>
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51 <test>
4
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52 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" />
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53 <param name="gene" value="BCL6" />
0
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54 <param name="radius" value="5" />
4
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55 <output name="outfile">
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56 <assert_contents>
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57 <has_line_matching expression="sample&#009;gene&#009;order_of_interaction&#009;interacting_gene.*" />
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58 </assert_contents>
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59 </output>
0
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 **What it does**
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64
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65 Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data.
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66 Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the
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67 protein itself. We have used the HPRD_ binary interaction data to build a p-p network graph which can be explored by GEMINI.
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68
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69 .. _HPRD: http://www.ncbi.nlm.nih.gov/pubmed/18988627
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70
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71 **Details**
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72
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73 *interactions: Find genes among variants that are interacting partners.*
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74
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75 Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data. Meaning to say that a damaging variant in an interacting partner of a potential protein may be equally interesting as the protein itself. We have used the HPRD binary interaction data to build a p-p network graph which can be explored by GEMINI.
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76
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77 **Examples**
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78
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79 EXAMPLE with setting -g CTBP2 and -r 3::
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80
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81 sample gene order_of_interaction interacting_gene
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82 M128215 CTBP2 0_order: CTBP2
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83 M128215 CTBP2 1_order: RAI2
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84 M128215 CTBP2 2_order: RB1
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85 M128215 CTBP2 3_order: TGM2,NOTCH2NL
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86
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87 Return CTBP2 (-g) interacting gene variants till the third order (-r)
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88
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89 EXAMPLE lof_interactions (use this option to restrict your analysis to only LoF variants); lof_interactions and -r 3::
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90
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91 sample lof_gene order_of_interaction interacting_gene
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92 M128215 TGM2 1_order: RB1
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93 M128215 TGM2 2_order: none
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94 M128215 TGM2 3_order: NOTCH2NL,CTBP2
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95
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96 Meaning to say return all LoF gene TGM2 (in sample M128215) interacting partners to a 3rd order of interaction.
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97
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98 EXAMPLE --var. An extended variant information (chrom, start, end etc.) for the interacting gene may be achieved with the –var option for both the interactions and the lof_interactions. Settings '-g CTBP2', '-r 3' and '--var'::
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99
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100 sample gene order_of_interaction interacting_gene var_id chrom start end impact biotype in_dbsnp clinvar_sig clinvar_disease_name aaf_1kg_all aaf_esp_all
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101 M128215 CTBP2 0 CTBP2 5 chr10 126678091 126678092 stop_gain protein_coding 1 None None None None
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102 M128215 CTBP2 1 RAI2 9 chrX 17819376 17819377 non_syn_coding protein_coding 1 None None 1 0.000473
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103 M128215 CTBP2 2 RB1 7 chr13 48873834 48873835 upstream protein_coding 1 None None 0.94 None
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104 M128215 CTBP2 3 NOTCH2NL 1 chr1 145273344 145273345 non_syn_coding protein_coding 1 None None None None
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105 M128215 CTBP2 3 TGM2 8 chr20 36779423 36779424 stop_gain protein_coding 0 None None None None
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106
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107 EXAMPLE with the following settings; '-r 3', '--var'::
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108
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109 sample lof_gene order_of_interaction interacting_gene var_id chrom start end impact biotype in_dbsnp clinvar_sig clinvar_disease_name aaf_1kg_all aaf_esp_all
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110 M128215 TGM2 1 RB1 7 chr13 48873834 48873835 upstream protein_coding 1 None None 0.94 None
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111 M128215 TGM2 3 NOTCH2NL 1 chr1 145273344 145273345 non_syn_coding protein_coding 1 None None None None
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112 M128215 TGM2 3 CTBP2 5 chr10 126678091 126678092 stop_gain protein_coding 1 None None None None
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113
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114 ]]></help>
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115 <expand macro="citations">
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116 <citation type="doi">10.1093/nar/gkn892</citation><!-- HPRD citation -->
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117 </expand>
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118 </tool>