Mercurial > repos > iuc > gemini_interactions

annotate gemini_interactions.xml @ 10:3030d363b6a8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit f7bdf08922aaf4119aefe7041e754a69cf64aebd
author iuc
date Wed, 13 Jul 2022 14:57:51 +0000
parents 2b371de05377
children
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@">
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2 <description>Find genes among variants that are interacting partners</description>
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2b371de05377 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemini commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>gemini_macros.xml</import>
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6 <token name="@BINARY@">interactions</token>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio">
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10 <!-- Fail loudly when the user-specified gene is unknown to gemini -->
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11 <regex match="Gene name not found or gene not in interaction file"
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12 source="stderr"
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13 level="fatal"
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14 description="The gene you specified is not defined in the interaction file" />
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15 </expand>
0
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16 <expand macro="version_command" />
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17 <command>
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18 <![CDATA[
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19 #if str($interactions.source) == 'preinstalled':
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20 #set $annotation_databases = $interactions.annotation_databases
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21 @PROVIDE_ANNO_DATA@
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22 #end if
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23
0
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24 gemini
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25 #set $gene = str($gene).strip()
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26 #if $gene:
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27 interactions -g '$gene'
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28 #else:
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29 ## lof interactions is a separate command line tool
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30 lof_interactions
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31 #end if
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32
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33 #if str($interactions.source) == 'history':
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34 --edges '${interactions.data}'
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35 #end if
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36
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37 -r $radius
0
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38 $variant_mode
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39
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40 '$infile'
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41 > '$outfile'
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42 ]]>
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43 </command>
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44 <inputs>
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45 <expand macro="infile" />
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46 <conditional name="interactions">
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47 <param name="source" type="select" label="Interaction data source"
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48 help="This tool requires a catalogue of known protein-protein interactions. Such interaction data, obtained from the Human Protein Reference Database (HPRD), is part of GEMINI's own annotation data, but you can choose to provide your own interactions data instead.">
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49 <option value="preinstalled">HPRD interaction data bundled with GEMINI</option>
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50 <option value="history">History dataset with interactions</option>
0
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51 </param>
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52 <when value="preinstalled">
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53 <expand macro="annotation_dir" />
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54 </when>
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55 <when value="history">
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56 <param name="data" type="data" format="txt"
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57 label="Interactions data"
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58 help="You can provide interaction data as a simple text file with one interaction of the form geneA|geneB (e.g., ZFPM2|GATA4) per line." />
0
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59 </when>
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60 </conditional>
6
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61 <param name="gene" type="text" value=""
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62 label="Report affected interaction partners of this particular gene"
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63 help="By default, the tool finds all genes affected by loss-of-function variants in your input, then, for every such gene, reports its interaction partners if they are also affected by any variant. If you specify the name of a gene of interest (e.g. PTPN22) here, you get the affected interaction partners of only this particular gene reported, irrespective of whether your gene of interest itself is affected by any variant or not." />
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64 <param argument="-r" name="radius" type="integer" value="3" min="0"
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65 label="Report interaction partners up to (and including) this order"
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66 help="A value of 1, for example, means: report only affected direct interaction partners. A value of 0 restricts the report to just variants in the query gene itself." />
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67 <param argument="--var" name="variant_mode" type="select" display="radio"
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68 label="Report format for interactions"
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69 help="">
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70 <option value="">Interaction partners only</option>
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71 <option value="--var">Interaction partners and the variants affecting them</option>
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72 </param>
0
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73 </inputs>
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74 <outputs>
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75 <data name="outfile" format="tabular" />
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76 </outputs>
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77 <tests>
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78 <test>
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79 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
0
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80 <param name="radius" value="5" />
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81 <output name="outfile">
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82 <assert_contents>
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83 <has_line line="sample&#009;lof_gene&#009;order_of_interaction&#009;interacting_gene" />
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84 <has_n_columns n="4" />
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85 </assert_contents>
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86 </output>
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87 </test>
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88 <test>
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89 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
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90 <param name="radius" value="5" />
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91 <param name="variant_mode" value="--var" />
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92 <output name="outfile">
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93 <assert_contents>
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94 <has_line_matching expression="sample&#009;lof_gene&#009;order_of_interaction&#009;interacting_gene.+" />
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95 </assert_contents>
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96 </output>
0
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97 </test>
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98 </tests>
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99 <help><![CDATA[
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100 **What it does**
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101
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102 Integrating the knowledge of the known protein-protein interactions would be useful in explaining variation data.
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103 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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104 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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105
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106 .. _HPRD: http://www.ncbi.nlm.nih.gov/pubmed/18988627
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107
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108 **Details**
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109
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110 *interactions: Find genes among variants that are interacting partners.*
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111
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112 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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113
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114 **Examples**
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115
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116 EXAMPLE with setting -g CTBP2 and -r 3::
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117
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118 sample gene order_of_interaction interacting_gene
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119 M128215 CTBP2 0_order: CTBP2
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120 M128215 CTBP2 1_order: RAI2
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121 M128215 CTBP2 2_order: RB1
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122 M128215 CTBP2 3_order: TGM2,NOTCH2NL
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123
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124 Return CTBP2 (-g) interacting gene variants till the third order (-r)
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125
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126 EXAMPLE lof_interactions (use this option to restrict your analysis to only LoF variants); lof_interactions and -r 3::
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127
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128 sample lof_gene order_of_interaction interacting_gene
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129 M128215 TGM2 1_order: RB1
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130 M128215 TGM2 2_order: none
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131 M128215 TGM2 3_order: NOTCH2NL,CTBP2
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132
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133 Meaning to say return all LoF gene TGM2 (in sample M128215) interacting partners to a 3rd order of interaction.
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134
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135 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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136
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137 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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138 M128215 CTBP2 0 CTBP2 5 chr10 126678091 126678092 stop_gain protein_coding 1 None None None None
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139 M128215 CTBP2 1 RAI2 9 chrX 17819376 17819377 non_syn_coding protein_coding 1 None None 1 0.000473
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140 M128215 CTBP2 2 RB1 7 chr13 48873834 48873835 upstream protein_coding 1 None None 0.94 None
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141 M128215 CTBP2 3 NOTCH2NL 1 chr1 145273344 145273345 non_syn_coding protein_coding 1 None None None None
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142 M128215 CTBP2 3 TGM2 8 chr20 36779423 36779424 stop_gain protein_coding 0 None None None None
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143
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144 EXAMPLE with the following settings; '-r 3', '--var'::
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145
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146 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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147 M128215 TGM2 1 RB1 7 chr13 48873834 48873835 upstream protein_coding 1 None None 0.94 None
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148 M128215 TGM2 3 NOTCH2NL 1 chr1 145273344 145273345 non_syn_coding protein_coding 1 None None None None
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149 M128215 TGM2 3 CTBP2 5 chr10 126678091 126678092 stop_gain protein_coding 1 None None None None
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150
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151 ]]></help>
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152 <expand macro="citations">
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153 <citation type="doi">10.1093/nar/gkn892</citation><!-- HPRD citation -->
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154 </expand>
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155 </tool>