Mercurial > repos > iuc > gprofiler_snpense

annotate gprofiler_snpense.xml @ 1:74385d563652 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit 4d4576623a85b58137f9e8c5a7747cb2f484c8b6"
author iuc
date Mon, 18 Nov 2019 17:55:27 -0500
parents f83a08dff6f0
children
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f83a08dff6f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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1 <?xml version="1.0"?>
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2 <tool id="gprofiler_snpense" name="gProfiler SNPense" version="@VERSION@">
f83a08dff6f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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3 <description>maps SNP rs-codes to gene names, chromosomal coordinates and variant effects</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"></expand>
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8 <expand macro="version_command" />
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9 <command detect_errors="aggressive">Rscript $script_file</command>
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10 <configfiles>
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11 <configfile name="script_file"><![CDATA[
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f83a08dff6f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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13 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
f83a08dff6f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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14 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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16 suppressPackageStartupMessages({
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17 library("gprofiler2")
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18 })
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20 set_user_agent(paste(get_user_agent(), "galaxy"))
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21 sessionInfo()
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23 #if $tool_settings.base_url
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24 set_base_url('${tool_settings.base_url}')
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25 #end if
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27 query <- scan('${input.file_name}', character(), quote = "")
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28
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29 response <- gsnpense( query
f83a08dff6f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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30 , filter_na = ${filter_na}
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31 )
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32
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33 output <- response
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34 output[['ensgs']] <- vapply(output[['ensgs']], paste, collapse = ",", character(1L))
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35 output[['gene_names']] <- vapply(output[['gene_names']], paste, collapse = ",", character(1L))
f83a08dff6f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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36
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37 output.colnames = append(colnames(output)[1:(length(colnames(output))-1)], colnames(output[['variants']]))
f83a08dff6f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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38 write.table(output, file='${output}', quote=FALSE, sep='\t', row.names = FALSE, col.names = output.colnames)
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39
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40 ]]></configfile>
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41 </configfiles>
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42 <inputs>
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43 <param name="input" type="data" format="txt" label="Input is whitespace-separated list of SNP IDs to be translated (should start with prefix ’rs’)." />
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44 <expand macro="filter_na" />
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45 <expand macro="tool_settings"></expand>
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46 </inputs>
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47 <outputs>
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48 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
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49 </outputs>
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50 <tests>
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51 <test>
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52 <param name="input" ftype="txt" value="example_snpense_query.txt" />
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53 <param name="base_url" value="http://biit.cs.ut.ee/gprofiler_archive3/e94_eg41_p11" />
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54 <output name="output" ftype="tabular" file="example_snpense_results.txt" sort="true" />
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55 </test>
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56 <test>
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57 <param name="input" ftype="txt" value="example_snpense_query.txt" />
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58 <param name="base_url" value="http://biit.cs.ut.ee/gprofiler_archive3/e94_eg41_p11" />
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59 <param name="filter_na" value="T" />
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60 <output name="output" ftype="tabular" file="example_snpense_results_2.txt" sort="true" />
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61 </test>
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62 </tests>
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63
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64 <help><![CDATA[
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65
f83a08dff6f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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66 **What it does**
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67 This tool wraps gprofiler2 R package which performs a request to g:Profiler g:SNPense tool through its API.
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68 g:Profiler g:SNPense maps SNP rs identifiers to chromosome positions, genes and variant effects. Available only
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69 for human SNPs.
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70
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71 -----
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72
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73 @REFERENCES@
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74
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75 ]]></help>
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76 <expand macro="citations"></expand>
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77 </tool>