Mercurial > repos > iuc > gprofiler_gost

annotate gprofiler_gost.xml @ 1:3e56960e2ca6 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 22:53:02 +0000
parents a7f523049880
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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diff changeset
1 <?xml version="1.0"?>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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2 <tool id="gprofiler_gost" name="gProfiler GOSt" version="@VERSION@">
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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3 <description>performs functional enrichment analysis of gene lists</description>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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4 <macros>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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5 <import>macros.xml</import>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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6 </macros>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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7 <edam_topics>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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8 <edam_topic>topic_0091</edam_topic>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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9 </edam_topics>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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10 <edam_operations>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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11 <edam_operation>operation_2436</edam_operation>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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12 </edam_operations>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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13 <expand macro="requirements"></expand>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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14 <expand macro="version_command" />
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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15 <command detect_errors="aggressive">Rscript $script_file</command>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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16 <configfiles>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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17 <configfile name="script_file"><![CDATA[
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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18
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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19 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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20 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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21
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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22 suppressPackageStartupMessages({
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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23 library("gprofiler2")
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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24 })
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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25
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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26 set_user_agent(paste(get_user_agent(), "galaxy"))
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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27 sessionInfo()
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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28
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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29 #if $tool_settings.base_url
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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30 set_base_url('${tool_settings.base_url}')
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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31 #end if
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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32
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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33 #if $advanced_options.custom_bg
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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34 custom_bg <- scan('${$advanced_options.custom_bg}', character(), quote = "")
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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35 #else
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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36 custom_bg = NULL
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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37 #end if
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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38
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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39 query <- scan('${input.file_name}', character(), quote = "")
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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40
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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41 sources <- c()
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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42
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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43 #if $data_sources.go_sources
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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44 #for $source in $data_sources.go_sources
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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45 #if $source
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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46 sources <- c(sources, '$source')
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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47 #end if
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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48 #end for
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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49 #end if
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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50
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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51 #if $data_sources.bp_sources
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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52 #for $source in $data_sources.bp_sources
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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53 #if $source
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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54 sources <- c(sources, '$source')
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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55 #end if
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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56 #end for
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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57 #end if
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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58
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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59 #if $data_sources.reg_sources
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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60 #for $source in $data_sources.reg_sources
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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61 #if $source
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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62 sources <- c(sources, '$source')
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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63 #end if
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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64 #end for
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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65 #end if
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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66
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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67 #if $data_sources.proto_sources
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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68 #for $source in $data_sources.proto_sources
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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69 #if $source
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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70 sources <- c(sources, '$source')
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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71 #end if
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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72 #end for
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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73 #end if
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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74
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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75 #if $data_sources.hp_sources
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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76 sources <- c(sources, '$data_sources.hp_sources')
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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77 #end if
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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78
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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79 if (length(sources) == 0) {
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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80 stop("No sources selected")
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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81 }
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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82
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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83
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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84 response <- gost( query
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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85 , organism = '${organism.organism}'
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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86 , ordered_query = $ordered_query
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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diff changeset
87 , significant = $advanced_options.significant
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
88 , exclude_iea = $data_sources.exclude_iea
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
89 , measure_underrepresentation = $advanced_options.measure_underrepresentation
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
90 , evcodes = $advanced_options.evcodes
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
91 , user_threshold = $advanced_options.user_threshold
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
92 , correction_method = '${advanced_options.correction_method}'
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
93 , domain_scope = '${advanced_options.domain_scope}'
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
94 , numeric_ns = '${advanced_options.numeric_ns}'
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
95 , custom_bg = custom_bg
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
96 , sources = sources
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
97 )
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
98
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
99 cat('\nversion:\n')
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
100 response[['meta']][['version']]
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
101
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
102 cat('\ntimestamp:\n')
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
103 response[['meta']][['timestamp']]
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
104
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
105 cat('\nquery metadata:\n')
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
106 response[['meta']][['query_metadata']]
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
107
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
108 output <- response[['result']]
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
109 output[['parents']] <- vapply(output[['parents']], paste, collapse = ",", character(1L))
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
110 output.colnames = colnames(output)
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
111 write.table(output, file='${output}', quote=FALSE, sep='\t', row.names = FALSE, col.names = output.colnames)
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
112
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
113 #if $tool_settings.export_plot
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
114 plot <- gostplot(response, capped = TRUE, interactive = TRUE)
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
115 htmlwidgets::saveWidget(plotly::as_widget(plot), '${plot}', selfcontained = TRUE)
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
116 #end if
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iuc
parents:
diff changeset
117
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
118 ]]></configfile>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
119 </configfiles>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
120 <inputs>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
121 <expand macro="input" />
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
122 <expand macro="organism" />
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
123
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
124 <param name="ordered_query" type="boolean" checked="false" truevalue="T" falsevalue="F" label="Ordered query" help="When input gene lists are ranked this option may be used to get GSEA style p-values." />
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
125
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
126 <section name="advanced_options" title="Advanced options" expanded="false">
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
127 <param name="significant" type="boolean" checked="true" truevalue="T" falsevalue="F" label="Significant only" help="Whether all or only statistically significant results should be returned." />
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
128 <param name="measure_underrepresentation" type="boolean" checked="false" truevalue="T" falsevalue="F" label="Measure underrepresentation" />
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
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129 <param name="evcodes" type="boolean" checked="false" truevalue="T" falsevalue="F" label="Evidence codes" help="Include evidence codes to the results. Note that this can decrease performance and make the query slower. In addition, a column ’intersection’ is created that contains the gene id-s that intersect between the query and term." />
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
130 <param name="user_threshold" type="float" value="0.05" label="User threshold" help="Custom p-value threshold, results with a larger p-value are excluded." />
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
131 <param name="correction_method" type="select" multiple="false" label="Correction method" help="The algorithm used for multiple testing correction.">
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
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132 <option selected="true" value="gSCS">g:SCS threshold</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
133 <option value="bonferroni">Bonferroni correction</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
134 <option value="fdr">Benjamini-Hochberg FDR</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
135 </param>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
136 <param name="domain_scope" type="select" multiple="false" label="Statistical domain scope" help="Effective genomic landscape for statistical testing.">
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
137 <option selected="true" value="annotated">Only annotated genes</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
138 <option value="known">All known genes</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
139 <option value="custom">Custom</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
140 </param>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
141 <param name="custom_bg" type="data" format="tabular" optional="true" label="Custom background" />
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
142 <param name="numeric_ns" type="text" value="" optional="true" label="Numeric IDs treated as" help="The prefix for fully numeric IDs. Check the “Resources” section below for the complete list of supported namespaces. E.g., ENTREZGENE_ACC, WIKIGENE_ACC." />
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
143 </section>
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diff changeset
144
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
145 <section name="data_sources" title="Data sources" expanded="false">
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
146 <param name="go_sources" type="select" multiple="true" display="checkboxes" optional="true" label="Gene Ontology">
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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diff changeset
147 <option selected="true" value="GO:BP">GO biological process</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
148 <option selected="true" value="GO:MF">GO molecular function</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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diff changeset
149 <option selected="true" value="GO:CC">GO cellular component</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
150 </param>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
151
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
152 <param name="exclude_iea" type="boolean" checked="false" truevalue="T" falsevalue="F" label="No electronic GO annotations" help="Exclude electronic GO annotations (IEA evidence code)." />
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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diff changeset
153
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
154 <param name="bp_sources" type="select" multiple="true" display="checkboxes" optional="true" label="biological pathways">
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
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155 <option selected="true" value="KEGG">KEGG</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
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156 <option selected="true" value="REAC">Reactome</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
157 <option selected="true" value="WP">WikiPathways</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
parents:
diff changeset
158 </param>
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159
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
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parents:
diff changeset
160 <param name="reg_sources" type="select" multiple="true" display="checkboxes" optional="true" label="regulatory motifs in DNA">
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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161 <option selected="true" value="TF">TRANSFAC</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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162 <option selected="true" value="MIRNA">miRTarBase</option>
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iuc
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163 </param>
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iuc
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164
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165 <param name="proto_sources" type="select" multiple="true" display="checkboxes" optional="true" label="protein databases">
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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166 <option selected="true" value="HPA">Human Protein Atlas</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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167 <option selected="true" value="CORUM">CORUM</option>
a7f523049880 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gprofiler/ commit ed9b518a6aaf6a5aada47e39c039f6936e41b290"
iuc
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168 </param>
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169
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170 <param name="hp_sources" type="select" multiple="true" display="checkboxes" optional="true" label="Human phenotype ontology">
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171 <option selected="true" value="HP">HP</option>
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172 </param>
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173 </section>
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174
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175 <expand macro="tool_settings">
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176 <param name="export_plot" type="boolean" checked="false" truevalue="T" falsevalue="F" label="Export plot" help="An interactive Plotly graph will be created alongside the tabular output. The plot is very similar to the one shown in the g:GOSt web tool." />
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177 </expand>
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178 </inputs>
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179 <outputs>
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180 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
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181
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182 <data name="plot" format="html" label="${tool.name} on ${on_string} (plot)">
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183 <filter>tool_settings['export_plot']</filter>
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184 </data>
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185 </outputs>
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186 <tests>
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187 <test>
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188 <param name="input" ftype="txt" value="example_query.txt" />
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189 <param name="base_url" value="http://biit.cs.ut.ee/gprofiler_archive3/e94_eg41_p11" />
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190 <output name="output" ftype="tabular" file="example_gost_results.txt" />
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191 </test>
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192 <test expect_num_outputs="2">
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193 <param name="input" ftype="txt" value="example_query_2.txt" />
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194 <param name="base_url" value="http://biit.cs.ut.ee/gprofiler_archive3/e94_eg41_p11" />
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195
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196 <conditional name="organism">
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197 <param name="organism" value="mmusculus" />
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198 </conditional>
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199
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200 <param name="ordered_query" value="T" />
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201 <param name="significant" value="F" />
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202 <param name="measure_underrepresentation" value="T" />
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203 <param name="evcodes" value="T" />
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204 <param name="user_threshold" value="0.1" />
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205 <param name="domain_scope" value="known" />
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206 <param name="correction_method" value="fdr" />
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207 <param name="numeric_ns" value="WIKIGENE_ACC" />
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208
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209 <section name="data_sources">
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210 <param name="go_sources" value="GO:MF,GO:CC" />
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211 <param name="exclude_iea" value="T" />
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212 <param name="bp_sources" />
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213 <param name="reg_sources" />
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214 <param name="proto_sources" />
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215 <param name="hp_sources" />
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216 </section>
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217
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218 <param name="export_plot" value="T" />
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219
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220 <output name="output" ftype="tabular" file="example_gost_results_2.txt" sort="true" />
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221 </test>
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222 </tests>
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223 <help><![CDATA[
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224 **What it does**
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225 This tool wraps gprofiler2 R package which performs a request to g:Profiler g:GOSt tool through its API.
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226 g:Profiler g:GOSt performs functional enrichment analysis of gene lists. The output is a table with the results
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227 and (optionally) a publication ready plot similar to the one shown in the g:GOSt web tool.
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228
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229 -----
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230
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231 @REFERENCES@
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232
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233 ]]></help>
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234 <expand macro="citations"></expand>
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235 </tool>