Mercurial > repos > iuc > gemini_interactions

comparison gemini_interactions.xml @ 6:47e49beb8e9b draft

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 62ed732cba355e695181924a8ed4cce49ca21c59
author iuc
date Fri, 11 Jan 2019 17:24:55 -0500
parents e8983ed311bf
children 2b371de05377
comparison
equal deleted inserted replaced
5:e8983ed311bf 6:47e49beb8e9b
3 <macros> 3 <macros>
4 <import>gemini_macros.xml</import> 4 <import>gemini_macros.xml</import>
5 <token name="@BINARY@">interactions</token> 5 <token name="@BINARY@">interactions</token>
6 </macros> 6 </macros>
7 <expand macro="requirements" /> 7 <expand macro="requirements" />
8 <expand macro="stdio" /> 8 <expand macro="stdio">
9 <!-- Fail loudly when the user-specified gene is unknown to gemini -->
10 <regex match="Gene name not found or gene not in interaction file"
11 source="stderr"
12 level="fatal"
13 description="The gene you specified is not defined in the interaction file" />
14 </expand>
9 <expand macro="version_command" /> 15 <expand macro="version_command" />
10 <command> 16 <command>
11 <![CDATA[ 17 <![CDATA[
12 @PROVIDE_ANNO_DATA@ 18 #if str($interactions.source) == 'preinstalled':
19 #set $annotation_databases = $interactions.annotation_databases
20 @PROVIDE_ANNO_DATA@
21 #end if
13 22
14 gemini 23 gemini
15 #if $gene.gene_selector == 'lof': 24 #set $gene = str($gene).strip()
16 ## lof interactions is a separate program 25 #if $gene:
26 interactions -g '$gene'
27 #else:
28 ## lof interactions is a separate command line tool
17 lof_interactions 29 lof_interactions
18 #else:
19 ## use normal gemini interactions program
20 @BINARY@
21 -g "${gene.gene}"
22 #end if 30 #end if
23 31
24 -r "${radius}" 32 #if str($interactions.source) == 'history':
33 --edges '${interactions.data}'
34 #end if
35
36 -r $radius
25 $variant_mode 37 $variant_mode
26 "${ infile }" 38
27 > "${ outfile }" 39 '$infile'
40 > '$outfile'
28 ]]> 41 ]]>
29 </command> 42 </command>
30 <inputs> 43 <inputs>
31 <expand macro="infile" /> 44 <expand macro="infile" />
32 45 <conditional name="interactions">
33 <conditional name="gene"> 46 <param name="source" type="select" label="Interaction data source"
34 <param name="gene_selector" type="select" label="Studying" help=""> 47 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.">
35 <option value="gene">Interesting gene</option> 48 <option value="preinstalled">HPRD interaction data bundled with GEMINI</option>
36 <option value="lof">All loss-of-function variants</option> 49 <option value="history">History dataset with interactions</option>
37 </param> 50 </param>
38 <when value="gene"> 51 <when value="preinstalled">
39 <param name="gene" type="text" label="Specify gene name" help="e.g. PTPN22 (-g)" /> 52 <expand macro="annotation_dir" />
40 </when> 53 </when>
41 <when value="lof"/> 54 <when value="history">
55 <param name="data" type="data" format="txt"
56 label="Interactions data"
57 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." />
58 </when>
42 </conditional> 59 </conditional>
43 <expand macro="annotation_dir" /> 60 <param name="gene" type="text" value=""
44 <expand macro="radius" /> 61 label="Report affected interaction partners of this particular gene"
45 <expand macro="variant_mode" /> 62 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." />
63 <param argument="-r" name="radius" type="integer" value="3" min="0"
64 label="Report interaction partners up to (and including) this order"
65 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." />
66 <param argument="--var" name="variant_mode" type="select" display="radio"
67 label="Report format for interactions"
68 help="">
69 <option value="">Interaction partners only</option>
70 <option value="--var">Interaction partners and the variants affecting them</option>
71 </param>
46 </inputs> 72 </inputs>
47 <outputs> 73 <outputs>
48 <data name="outfile" format="tabular" /> 74 <data name="outfile" format="tabular" />
49 </outputs> 75 </outputs>
50 <tests> 76 <tests>
51 <test> 77 <test>
52 <param name="infile" value="gemini_load_result1.db" ftype="gemini.sqlite" /> 78 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
53 <param name="gene" value="BCL6" />
54 <param name="radius" value="5" /> 79 <param name="radius" value="5" />
55 <output name="outfile"> 80 <output name="outfile">
56 <assert_contents> 81 <assert_contents>
57 <has_line_matching expression="sample&#009;gene&#009;order_of_interaction&#009;interacting_gene.*" /> 82 <has_line line="sample&#009;lof_gene&#009;order_of_interaction&#009;interacting_gene" />
83 <has_n_columns n="4" />
84 </assert_contents>
85 </output>
86 </test>
87 <test>
88 <param name="infile" value="gemini_comphets_input.db" ftype="gemini.sqlite" />
89 <param name="radius" value="5" />
90 <param name="variant_mode" value="--var" />
91 <output name="outfile">
92 <assert_contents>
93 <has_line_matching expression="sample&#009;lof_gene&#009;order_of_interaction&#009;interacting_gene.+" />
58 </assert_contents> 94 </assert_contents>
59 </output> 95 </output>
60 </test> 96 </test>
61 </tests> 97 </tests>
62 <help><![CDATA[ 98 <help><![CDATA[