annotate egsea.xml @ 2:ba2111ae6eb4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
author iuc
date Mon, 28 Jan 2019 18:39:06 -0500
parents 73281fbdf6c1
children 31ea4992b948
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ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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1 <tool id="egsea" name="EGSEA" version="1.8.0">
0
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2 <description> easy and efficient ensemble gene set testing</description>
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3 <requirements>
2
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4 <requirement type="package" version="1.8.0">bioconductor-egsea</requirement>
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5 <requirement type="package" version="1.6.0">r-optparse</requirement>
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6 <requirement type="package" version="0.2.20">r-rjson</requirement>
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7 <!--statmod is required for fry-->
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8 <requirement type="package" version="1.4.30">r-statmod</requirement>
0
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9 </requirements>
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10 <version_command><![CDATA[
1
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11 echo $(R --version | grep version | grep -v GNU)", EGSEA version" $(R --vanilla --slave -e "library(EGSEA); cat(sessionInfo()\$otherPkgs\$EGSEA\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
0
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12 ]]></version_command>
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13 <command detect_errors="exit_code"><![CDATA[
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14 ## EGSEA requires at least 2 threads
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15 SLOTS=\${GALAXY_SLOTS:-2};
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16 [ "\$SLOTS" -eq 1 ] && SLOTS=2;
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17
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18 mkdir ./report_dir &&
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19 mkdir '$outReport.extra_files_path' &&
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20
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21 Rscript '$__tool_directory__/egsea.R'
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22
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23 --threads \$SLOTS
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24
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25 #if $input.format=="files":
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26
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27 ## Adapted from DESeq2 wrapper
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28 #import json
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29 #set $temp_factor_names = list()
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30 #for $fact in $input.rep_factor:
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31 #set $temp_factor = list()
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32 #for $g in $fact.rep_group:
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33 #set $count_files = list()
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34 #for $file in $g.countsFile:
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35 $count_files.append(str($file))
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36 #end for
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37 $temp_factor.append( {str($g.groupName): $count_files} )
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38 #end for
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39
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40 $temp_factor.reverse()
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41 $temp_factor_names.append([str($fact.factorName), $temp_factor])
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42 #end for
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43 --filesPath '#echo json.dumps(temp_factor_names)#'
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44
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45 #elif $input.format=="matrix":
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46 --matrixPath '$input.counts'
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47 #if $input.fact.ffile=='yes':
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48 --factFile '$input.fact.finfo'
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49 #else:
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50 --factInput '${ '|'.join( ['%s::%s' % ($x.factorName, $x.groupNames) for x in $input.fact.rep_factor] ) }'
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51 #end if
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52 #end if
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53
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54 --contrastData '${ ','.join( ['%s' % $x.contrast for x in $rep_contrast] ) }'
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55
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56 --genes '$genes'
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57 --species $species
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58
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59 --base_methods $base_methods
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60 --msigdb $msigdb.msigdb_gsets
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61 --keggdb $keggdb.keggdb_gsets
1
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62 --keggupdated $keggdb.kegg_updated
0
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63 --gsdb $gsdb.gsdb_gsets
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64
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65 --display_top $advanced.display_top
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66 --min_size $advanced.min_size
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67 --fdr_cutoff $advanced.fdr_cutoff
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68 --combine_method $advanced.combine_method
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69 --sort_method $advanced.sort_method
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70
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71 --rdaOpt $advanced.rdaOpt
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72
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73 && cp ./report_dir/index.html '$outReport'
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74 && cp -r ./report_dir/* '$outReport.extra_files_path'
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75
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76 #if $advanced.rscriptOpt:
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77 && cp '$__tool_directory__/egsea.R' '$outRscript'
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78 #end if
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79
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80 ]]></command>
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81 <inputs>
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82
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83 <!-- Counts and Factors -->
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84 <conditional name="input">
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85 <param name="format" type="select" label="Count Files or Matrix?"
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86 help="You can choose to input either separate count files (one per sample) or a single count matrix">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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parents:
diff changeset
87 <option value="files">Separate Count Files</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
88 <option value="matrix">Single Count Matrix</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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parents:
diff changeset
89 </param>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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parents:
diff changeset
90
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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parents:
diff changeset
91 <when value="files">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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parents:
diff changeset
92 <repeat name="rep_factor" title="Factor" min="1">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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93 <param name="factorName" type="text" label="Name" help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Optional additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section for more information. NOTE: Please only use letters, numbers or underscores.">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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parents:
diff changeset
94 <sanitizer>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
95 <valid initial="string.letters,string.digits"><add value="_" /></valid>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
96 </sanitizer>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
97 </param>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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parents:
diff changeset
98 <repeat name="rep_group" title="Group" min="2" default="2">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
99 <param name="groupName" type="text" label="Name"
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
100 help="Name of group that the counts files(s) belong to (e.g. WT or Mut). NOTE: Please only use letters, numbers or underscores (case sensitive).">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
101 <sanitizer>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
102 <valid initial="string.letters,string.digits"><add value="_" /></valid>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
103 </sanitizer>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
104 </param>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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105 <param name="countsFile" type="data" format="tabular" multiple="true" label="Counts file(s)"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
106 </repeat>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
107 </repeat>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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108 </when>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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109
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
110 <when value="matrix">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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111 <param name="counts" type="data" format="tabular" label="Count Matrix"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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parents:
diff changeset
112
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
113 <conditional name="fact">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
114 <param name="ffile" type="select" label="Input factor information from file?"
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
115 help="You can choose to input the factor and group information for the samples from a file or manually enter below.">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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116 <option value="no">No</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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117 <option value="yes">Yes</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
118 </param>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
119 <when value="yes">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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120 <param name="finfo" type="data" format="tabular" label="Factor File"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
121 </when>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
122 <when value="no" >
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
123 <repeat name="rep_factor" title="Factor" min="1">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
124 <param name="factorName" type="text" label="Factor Name"
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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125 help="Name of experiment factor of interest (e.g. Genotype). One factor must be entered and there must be two or more groups per factor. Additional factors (e.g. Batch) can be entered using the Insert Factor button below, see Help section below. NOTE: Please only use letters, numbers or underscores.">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
126 <validator type="empty_field" />
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
127 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w]+$</validator>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
128 </param>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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129 <param name="groupNames" type="text" label="Groups"
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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130 help="Enter the group names for the samples separated with commas e.g. WT,WT,WT,Mut,Mut,Mut. The order of the names must match the order of the samples in the columns of the count matrix. NOTE: Please only use letters, numbers or underscores (case sensitive).">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
131 <validator type="empty_field" />
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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132 <validator type="regex" message="Please only use letters, numbers or underscores, and separate levels by commas">^[\w,]+$</validator>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
133 </param>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
134 </repeat>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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135 </when>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
136 </conditional>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
137 </when>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
138 </conditional>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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139
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
140 <!-- Contrasts -->
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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141 <repeat name="rep_contrast" title="Contrast" min="1" default="1">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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142 <param name="contrast" type="text" label="Contrast of Interest" help="Names of two groups to compare separated by a hyphen e.g. Mut-WT. If the order is Mut-WT the fold changes in the results will be up/down in Mut relative to WT. If you have more than one contrast enter each separately using the Insert Contrast button below. For more info, see Chapter 8 in the limma User's guide: https://www.bioconductor.org/packages/release/bioc/vignettes/limma/inst/doc/usersguide.pdf">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
143 <validator type="empty_field" />
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
144 <validator type="regex" message="Please only use letters, numbers or underscores">^[\w-]+$</validator>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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145 </param>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
146 </repeat>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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147
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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148 <param name="genes" type="data" format="tabular"
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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149 label="Symbols Mapping file"
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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150 help="A file of Entrez Gene IDs mapped to Gene symbols in the format shown in the Help section below."/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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151
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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152 <param name="species" type="select" label="Species" help="Default: Human">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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153 <option value="human" selected="True">Human</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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154 <option value="mouse">Mouse</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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155 <option value="rat">Rat</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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156 </param>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
157
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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158 <param name="base_methods" type="select" display="checkboxes" multiple="True" min="3" label="Gene Set Testing Methods" help="Select at least 3 gene set testing methods">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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159 <option value="camera" selected="True">camera</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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160 <option value="safe">safe</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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161 <option value="gage">gage</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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162 <option value="zscore">zscore</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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163 <option value="gsva">gsva</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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164 <option value="globaltest" selected="True">globaltest</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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165 <option value="ora" selected="True">ora</option>
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166 <option value="ssgsea">ssgsea</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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167 <option value="padog">padog</option>
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168 <option value="plage">plage</option>
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169 <option value="fry">fry</option>
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170 <option value="roast">roast</option>
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171 </param>
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172
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173 <section name="msigdb" title="MSigDB Gene Sets" expanded="True">
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174 <param name="msigdb_gsets" type="select" display="checkboxes" optional="True" multiple="True" label="MSigDB Gene Set Collections" help="Choose any MSigDB Gene Set Collections you want to use. Default: H: hallmark gene sets">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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175 <option value="h" selected="True">H: hallmark gene sets</option>
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176 <option value="c1">C1: positional gene sets (human only)</option>
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177 <option value="c2">C2: curated gene sets</option>
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178 <option value="c3">C3: motif gene sets</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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179 <option value="c4">C4: computational gene sets</option>
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180 <option value="c5">C5: GO gene sets</option>
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181 <option value="c6">C6: oncogenic gene sets</option>
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182 <option value="c7">C7: immunologic gene sets</option>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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183 </param>
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184 </section>
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185
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186 <section name="keggdb" title="KEGG Pathways" expanded="True">
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187 <param name="keggdb_gsets" type="select" display="checkboxes" optional="True" multiple="True" label="KEGG Pathways" help="Choose any KEGG Pathways you want to use. Default: None">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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188 <option value="keggmet">Metabolism pathways</option>
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189 <option value="keggsig">Signalling pathways</option>
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190 <option value="keggdis">Disease pathways</option>
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191 </param>
1
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192 <param name="kegg_updated" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Download KEGG pathways?" help="Select Yes if you want to download the most recent KEGG pathways, see the Help section below. Default: No"/>
0
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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193 </section>
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194
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195 <section name="gsdb" title="GeneSetDB Gene Sets" expanded="True">
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196 <param name="gsdb_gsets" type="select" display="checkboxes" optional="True" multiple="True" label="GeneSigDB Gene Set Collections" help="Choose any GeneSetDB Gene Set Collections you want to use. Default: None">
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197 <option value="gsdbpath">Pathway collection</option>
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198 <option value="gsdbdis">Disease/Phenotype collection</option>
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199 <option value="gsdbdrug">Drug/Chemical collection</option>
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200 <option value="gsdbreg">Gene Regulation collection</option>
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201 <option value="gsdbgo">Gene Ontology collection</option>
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202 </param>
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203 </section>
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204
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205 <section name="advanced" title="Advanced Options">
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206 <param name="display_top" type="integer" value="5" min="1" max="20" label="Top Gene Sets to display" help="Set the number of top gene sets to display. Increasing this number increases the time to run, in order to generate the additional plots etc."/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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207 <param name="min_size" type="integer" min="0" value="2" label="Minimum Size of Gene Set" help="Minimum size of a gene set to be included in the analysis. Default: 2" />
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208 <param name="fdr_cutoff" type="float" value="0.05" min="0" max="1" label="FDR cutoff" help="Cut-off threshold of differentially expressed genes used for the calculation of Significance Score and Regulation Direction. Default: 0.05"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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209 <param name="combine_method" type="select" label="Combine Method" help="Method to use to combine the p-values from the different gene set testing methods. Default: wilkinson">
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210 <option value="wilkinson" selected="True">wilkinson</option>
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211 <option value="fisher">fisher</option>
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212 <option value="average">average</option>
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213 <option value="logitp">logitp</option>
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214 <option value="sump">sump</option>
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215 <option value="sumz">sumz</option>
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216 <option value="votep">votep</option>
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217 <option value="median">median</option>
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218 </param>
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219 <param name="sort_method" type="select" label="Sort Method" help="Select method to sort the results. Any of EGSEA’s combined scores or the rankings from individual base methods can be used for sorting the results. Default: med.rank">
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220 <option value="p.adj">p.adj</option>
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221 <option value="p.value">p.value</option>
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222 <option value="vote.rank">vote.rank</option>
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223 <option value="avg.rank">avg.rank</option>
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224 <option value="med.rank" selected="True">med.rank</option>
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225 <option value="min.pvalue">min.pvalue</option>
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226 <option value="min.rank">min.rank</option>
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227 <option value="avg.logfc">avg.logfc</option>
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228 <option value="avg.logfc.dir">avg.logfc.dir</option>
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229 <option value="direction">direction</option>
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230 <option value="significance">significance</option>
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231 <option value="camera">camera</option>
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232 <option value="roast">roast</option>
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233 <option value="safe" >safe</option>
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234 <option value="gage">gage</option>
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235 <option value="padog">padog</option>
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236 <option value="plage">plage</option>
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237 <option value="zscore">zscore</option>
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238 <option value="gsva">gsva</option>
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239 <option value="ssgsea">ssgsea</option>
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240 <option value="globaltest">globaltest</option>
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241 <option value="ora">ora</option>
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242 <option value="fry">fry</option>
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243 </param>
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244 <param name="rscriptOpt" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output Rscript?" help="If this option is set to Yes, the Rscript used will be provided as a text file in the output. Default: No"/>
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245 <param name="rdaOpt" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Output RData file?" help="Output all the data used by R in the analysis, can be loaded into R. Default: No" />
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246 </section>
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247 <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False">
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248 <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator>
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249 </param>
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250 </inputs>
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251
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252 <outputs>
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253 <data name="outReport" format="html" label="${tool.name} on ${on_string}: Report"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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254 <collection name="outTables" type="list" label="${tool.name} on ${on_string}: Tables">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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255 <discover_datasets pattern="(?P&lt;name&gt;.+)\.txt$" format="tabular" directory="report_dir/ranked-gene-sets-base" visible="false" />
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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256 </collection>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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257 <data name="outRscript" format="txt" from_work_dir="*.txt" label="${tool.name} on ${on_string}: Rscript">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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258 <filter>advanced['rscriptOpt'] is True</filter>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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259 </data>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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260 <data name="outRdata" format="rdata" from_work_dir="EGSEA_analysis.RData" label="${tool.name} on ${on_string}: RData file">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
261 <filter>advanced['rdaOpt'] is True</filter>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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262 </data>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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263 </outputs>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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264
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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265 <tests>
1
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parents: 0
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266 <!-- Ensure report is output -->
2
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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parents: 1
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267 <test expect_num_outputs="2">
0
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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268 <param name="non_commercial_use" value="True"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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269 <param name="format" value="matrix" />
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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270 <param name="counts" value="il13.counts"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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271 <param name="genes" value="il13.genes"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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272 <repeat name="rep_factor">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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273 <param name="factorName" value="Treatment"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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274 <param name="groupNames" value="IL13,IL13Ant,IL13,IL13,IL13Ant"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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275 </repeat>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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276 <repeat name="rep_contrast">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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277 <param name="contrast" value="IL13Ant-IL13"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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278 </repeat>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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279 <output_collection name="outTables" count="1">
2
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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parents: 1
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280 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular">
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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281 <assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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282 <has_text_matching expression="Rank.*ID.*GeneSet.*BroadUrl.*Description.*PubMedID.*NumGenes.*Contributor.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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parents: 1
diff changeset
283 <has_text_matching expression="1.*M5890.*HALLMARK_TNFA_SIGNALING_VIA_NFKB.*181/200.*3.6" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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diff changeset
284 </assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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285 </element>
0
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
286 </output_collection>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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287 <output name="outReport">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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288 <assert_contents>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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289 <has_text text="Gene Set Testing Report"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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290 </assert_contents>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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291 </output>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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292 </test>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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293 <!-- Ensure factors file input works and Rscript is output-->
2
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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parents: 1
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294 <test expect_num_outputs="3">
0
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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295 <param name="non_commercial_use" value="True"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
296 <param name="format" value="matrix"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
297 <param name="counts" value="il13.counts"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
298 <param name="genes" value="il13.genes"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
299 <param name="ffile" value="yes"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
300 <param name="finfo" value="il13.group"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
301 <repeat name="rep_contrast">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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302 <param name="contrast" value="IL13Ant-IL13" />
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
303 </repeat>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
304 <param name="rscriptOpt" value="True"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
305 <output name="outReport">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
306 <assert_contents>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
307 <has_text text="Gene Set Testing Report"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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308 </assert_contents>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
309 </output>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
310 <output_collection name="outTables" count="1">
2
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
311 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular">
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
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diff changeset
312 <assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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313 <has_text_matching expression="Rank.*ID.*GeneSet.*BroadUrl.*Description.*PubMedID.*NumGenes.*Contributor.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
314 <has_text_matching expression="1.*M5890.*HALLMARK_TNFA_SIGNALING_VIA_NFKB.*181/200.*3.6" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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diff changeset
315 </assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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diff changeset
316 </element>
0
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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317 </output_collection>
2
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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318 <output name="outRscript">
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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319 <assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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320 <has_text_matching expression="save.image" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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321 </assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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diff changeset
322 </output>
0
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
323 </test>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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324 <!-- Ensure two contrasts works -->
2
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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parents: 1
diff changeset
325 <test expect_num_outputs="2">
0
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
326 <param name="non_commercial_use" value="True"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
327 <param name="format" value="matrix"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
328 <param name="counts" value="il13.counts"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
329 <param name="genes" value="il13.genes"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
330 <param name="ffile" value="yes"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
331 <param name="finfo" value="il13.group"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
332 <repeat name="rep_contrast">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
333 <param name="contrast" value="IL13Ant-IL13"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
334 </repeat>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
335 <repeat name="rep_contrast">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
336 <param name="contrast" value="IL13-IL13Ant"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
337 </repeat>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
338 <output_collection name="outTables" count="3">
2
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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339 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular">
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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340 <assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
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341 <has_text_matching expression="Rank.*ID.*GeneSet.*BroadUrl.*Description.*PubMedID.*NumGenes.*Contributor.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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342 <has_text_matching expression="1.*M5890.*HALLMARK_TNFA_SIGNALING_VIA_NFKB.*181/200.*3.6" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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343 </assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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344 </element>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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345 <element name="ranked-h-gene-sets-IL13-IL13Ant" ftype="tabular">
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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346 <assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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347 <has_text_matching expression="Rank.*ID.*GeneSet.*BroadUrl.*Description.*PubMedID.*NumGenes.*Contributor.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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348 <has_text_matching expression="1.*M5890.*HALLMARK_TNFA_SIGNALING_VIA_NFKB.*181/200.*3.6" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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349 </assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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350 </element>
0
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
351 </output_collection>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
352 </test>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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353 <!-- Ensure two factors works -->
2
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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354 <test expect_num_outputs="2">
0
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
355 <param name="non_commercial_use" value="True"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
356 <param name="format" value="matrix"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
357 <param name="counts" value="il13.counts"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
358 <param name="genes" value="il13.genes"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
359 <param name="ffile" value="yes"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
360 <param name="finfo" value="il13.group_batch"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
361 <repeat name="rep_contrast">
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
362 <param name="contrast" value="IL13Ant-IL13"/>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
363 </repeat>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
364 <output_collection name="outTables" count="1">
2
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
365 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular">
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
366 <assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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367 <has_text_matching expression="Rank.*ID.*GeneSet.*BroadUrl.*Description.*PubMedID.*NumGenes.*Contributor.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
368 <has_text_matching expression="1.*M5928.*HALLMARK_MYC_TARGETS_V2.*53/58.*6.7" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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369 </assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
370 </element>
0
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
371 </output_collection>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
372 </test>
1
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
373 <!-- Ensure all gene set methods work -->
2
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
374 <test expect_num_outputs="2">
1
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
375 <param name="non_commercial_use" value="True"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
376 <param name="format" value="matrix"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
377 <param name="counts" value="il13.counts"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
378 <param name="genes" value="il13.genes"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
379 <param name="ffile" value="yes"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
380 <param name="finfo" value="il13.group_batch"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
381 <repeat name="rep_contrast">
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
382 <param name="contrast" value="IL13Ant-IL13"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
383 </repeat>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
384 <param name="base_methods" value="camera,safe,gage,zscore,gsva,globaltest,ora,ssgsea,padog,plage,fry,roast"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
385 <output_collection name="outTables" count="1">
2
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
386 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular">
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
387 <assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
388 <has_text_matching expression="Rank.*ID.*GeneSet.*BroadUrl.*Description.*PubMedID.*NumGenes.*Contributor.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
389 <has_text_matching expression="1.*M5928.*HALLMARK_MYC_TARGETS_V2.*53/58.*2.6" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
390 </assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
391 </element>
1
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
392 </output_collection>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
393 </test>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
394 <!-- Ensure KEGG updated works -->
2
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
395 <test expect_num_outputs="2">
1
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
396 <param name="non_commercial_use" value="True"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
397 <param name="format" value="matrix"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
398 <param name="counts" value="il13.counts"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
399 <param name="genes" value="il13.genes"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
400 <param name="ffile" value="yes"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
401 <param name="finfo" value="il13.group_batch"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
402 <repeat name="rep_contrast">
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
403 <param name="contrast" value="IL13Ant-IL13"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
404 </repeat>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
405 <param name="keggdb_gsets" value="keggmet"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
406 <param name="kegg_updated" value="True"/>
73281fbdf6c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 225518a08941e7ef8e5c402e3696ec5fa6e592a0
iuc
parents: 0
diff changeset
407 <output_collection name="outTables" count="2">
2
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
408 <element name="ranked-kegg-gene-sets-IL13Ant-IL13" ftype="tabular">
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
409 <assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
410 <has_text_matching expression="Rank.*ID.*GeneSet.*NumGenes.*Type.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
411 <has_text_matching expression="1.*hsa00290.*Valine, leucine and isoleucine biosynthesis.*4/4.*Metabolism.*5.1" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
412 </assert_contents>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
413 </element>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
414 </output_collection>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
415 </test>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
416 <!-- Ensure individual counts files works -->
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
417 <test expect_num_outputs="2">
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
418 <param name="non_commercial_use" value="True"/>
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
diff changeset
419 <param name="format" value="files" />
ba2111ae6eb4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit ee9b940a5ffa6c52e42a89e55c0f5bdda0a386d5
iuc
parents: 1
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420 <repeat name="rep_factor">
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421 <param name="factorName" value="Treatment"/>
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422 <repeat name="rep_group">
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423 <param name="groupName" value="IL13"/>
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424 <param name="countsFile" value="IL13-1.counts,IL13-2.counts,IL13-3.counts"/>
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425 </repeat>
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426 <repeat name="rep_group">
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427 <param name="groupName" value="IL13Ant"/>
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428 <param name="countsFile" value="IL13Ant-1.counts,IL13Ant-2.counts"/>
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429 </repeat>
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430 </repeat>
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431 <repeat name="rep_factor">
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432 <param name="factorName" value="Batch"/>
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433 <repeat name="rep_group">
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434 <param name="groupName" value="b1"/>
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435 <param name="countsFile" value="IL13-1.counts,IL13Ant-1.counts"/>
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436 </repeat>
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437 <repeat name="rep_group">
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438 <param name="groupName" value="b2"/>
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439 <param name="countsFile" value="IL13-2.counts,IL13-3.counts,IL13Ant-2.counts"/>
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440 </repeat>
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441 </repeat>
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442 <param name="genes" value="il13.genes"/>
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443 <repeat name="rep_contrast">
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444 <param name="contrast" value="IL13Ant-IL13"/>
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445 </repeat>
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446 <output_collection name="outTables" count="1">
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447 <element name="ranked-h-gene-sets-IL13Ant-IL13" ftype="tabular">
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448 <assert_contents>
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449 <has_text_matching expression="Rank.*ID.*GeneSet.*BroadUrl.*Description.*PubMedID.*NumGenes.*Contributor.*p.value.*p.adj.*vote.rank.*avg.rank.*med.rank.*min.pvalue.*min.rank.*avg.logfc.*avg.logfc.dir.*direction.*significance.*camera.*globaltest.*ora" />
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450 <has_text_matching expression="1.*M5928.*HALLMARK_MYC_TARGETS_V2.*53/58.*6.7" />
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451 </assert_contents>
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452 </element>
1
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453 </output_collection>
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454 </test>
0
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455 </tests>
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456
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457 <help><![CDATA[
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458
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459 .. class:: infomark
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460
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461 **What it does**
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462
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463 EGSEA_, an acronym for *Ensemble of Gene Set Enrichment Analyses*, is a `Bioconductor package`_ that utilizes the analysis results of eleven prominent GSE algorithms from the literature to calculate collective significance scores for gene sets. These methods are currently: **ora, globaltest, plage, safe, zscore, gage, ssgsea, roast, fry, padog, camera, gsva**. The ora, gage, camera and gsva methods depend on a competitive null hypothesis while the remaining seven methods are based on a self-contained hypothesis. EGSEA’s gene set database, the **EGSEAdata** Bioconductor package, contains around 25,000 gene sets from 16 collections from MSigDB_, KEGG_ and GeneSetDB_. Supported organisms are human, mouse and rat, however MSigDB is only available for human and mouse. An example `EGSEA workflow`_ is available at the Bioconductor workflows website.
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464
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465 Currently the **egsea.cnt** function is implemented in this tool. This function takes a raw RNA-Seq count matrix and uses **limma-voom** with TMM normalization to convert the RNA-seq counts into expression values for EGSEA analysis.
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466
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467 EGSEA returns a HTML report of detailed analysis results for each contrast of interest and comparative analysis results. The heatmap view at both the gene set and summary level and the summary level bar plots can be useful summaries to include in publications to highlight the gene set testing results.
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468
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469 .. class:: warningmark
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470
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471 **WARNING: This tool is only available for non-commercial use.**
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472
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473 The **GAGE** and **Pathview** packages used by EGSEA make use of KEGG data
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474 and Non-academic uses may require a KEGG license agreement. Before using, be
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475 sure to review, agree, and comply with the relevant licenses for KEGG and
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476 MSigDB.
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477
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478 * `KEGG Licence`_
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479 * `MSigDB Licence`_
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480
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481 .. _KEGG Licence: http://www.kegg.jp/kegg/legal.html
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482 .. _MSigDB Licence: http://software.broadinstitute.org/gsea/license_terms_list.jsp
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483
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484 -----
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485
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486 **Inputs**
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487
2
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488 **Counts Data**
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489
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490 This tool requires a counts matrix (counts table) containing the raw RNA-seq read counts. The counts data can either be input as separate counts files (one sample per file) or a single count matrix (one sample per column). The rows correspond to genes, and columns correspond to the counts for the samples. Values must be tab separated, with the first row containing the sample/column labels. The first column must contain Entrez Gene IDs that are unique (not repeated) within the counts file. Entrez IDs can be obtained from the **annotateMyIDs** Galaxy tool. Genes with low counts should be removed, such as in the filtered counts matrix that can be output from the **limma** tool.
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491
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492 Example - **Separate Count Files**:
0
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493
2
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494 =============== ==========
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495 EntrezID **WT1**
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496 =============== ==========
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497 1 71
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498 1000 3
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499 10000 2310
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500 100009605 3
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501 100009613 9
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502 =============== ==========
0
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503
2
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504 Example - **Single Count Matrix**:
0
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505
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506 =============== ========== ========== ========== ========= ========= =========
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507 EntrezID **WT1** **WT2** **WT3** **Mut1** **Mut2** **Mut3**
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508 =============== ========== ========== ========== ========= ========= =========
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509 1 71 73 69 36 22 28
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510 1000 3 4 2 4 0 1
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511 10000 2310 2142 2683 1683 2068 2172
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512 100009605 3 1 2 1 5 3
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513 100009613 9 11 4 13 6 10
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514 =============== ========== ========== ========== ========= ========= =========
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515
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516 **Factor Information**
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517
2
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518 Enter factor names and groups in the tool form, or provide a tab-separated file that has the names of the samples in the first column and one header row. The sample names must be the same as the names in the columns of the count matrix. The second column should contain the primary factor levels (e.g. WT, Mut) with optional additional columns for any secondary factors e.g Batch.
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519
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520 Example:
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521
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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522 ========== ============ =========
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523 **Sample** **Genotype** **Batch**
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524 ---------- ------------ ---------
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525 WT1 WT b1
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526 WT2 WT b2
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527 WT3 WT b3
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528 Mut1 Mut b1
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529 Mut2 Mut b2
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530 Mut3 Mut b3
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531 ========== ============ =========
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532
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533 *Factor Name:* The name of the experimental factor being investigated e.g. Genotype, Treatment. One factor must be entered and spaces must not be used. Optionally, additional factors can be included, these are variables that might influence your experiment e.g. Batch, Gender, Subject. If additional factors are entered, edgeR will fit an additive linear model.
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534
2
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535 *Groups:* The names of the groups for the factor. Spaces must not be used and if entered into the tool form above, the values should be separated by commas.
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536
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537 **Symbols Mapping file**
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538
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539 A file containing the Gene Symbol for each Entrez Gene ID. The first column must be the Entrez Gene IDs and the second column must be the Gene Symbols. It is used for the heatmap visualization. The number of rows should match that of the Counts Matrix.
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540
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541 Example:
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542
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543 ========= =========
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544 EntrezID Symbols
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545 ========= =========
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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546 1 A1BG
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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547 1000 CDH2
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548 10000 AKT3
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549 100009605 TRNAF1
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550 100009613 ANO1-AS2
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551 ========= =========
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552
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553 -----
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554
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555 **Outputs**
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556
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557 The EGSEA report is an interactive HTML report that is generated to enable a swift navigation through the results of an EGSEA analysis. The pages below are generated for each gene set collection and contrast/comparison.
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558
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559 **Stats Table page**
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560
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561 The Stats Table page shows the detailed statistics of the EGSEA analysis for the top gene sets. It shows the EGSEA scores, individual rankings and additional annotation for each gene set. Hyperlinks to the source of each gene set can be seen in this table when they are available. The "Direction" column shows the regulation direction of a gene set which is calculated based on the logFC, which is either calculated from the limma differential expression analysis or provided by the user. The logFC cutoff and FDR cutoff are applied for this calculation. The calculations of the EGSEA scores can be seen in the references section. The method topSets can be used to generate custom Stats Table.
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562
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563 **Heatmaps page**
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564
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565 The Heatmaps page shows the heatmaps of the gene fold changes for the gene sets that are presented in the Stats Table page. Red indicates up-regulation while blue indicates down-regulation. Only genes that appear in the input expression/count matrix are visualized in the heat map. Gene names are coloured based on their statistical significance in the limma differential expression analysis. The "Interpret Results" link below each heat map allows the user to download the original heat map values along with additional statistics from limma DE analysis ( if available) so that they can be used to perform further analysis in R, e.g., customizing the heat map visualization.
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566
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567 **Summary Plots page**
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568
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569 The Summary Plots page shows the methods ranking plot along with the summary plots of EGSEA analysis. The method plot uses multidimensional scaling (MDS) to visualize the ranking of individual methods on a given gene set collection. The summary plots are bubble plots that visualize the distribution of gene sets based on the EGSEA Significance Score and another EGSEA score (default, p-value). Two summary plots are generated: ranking and directional plots. Each gene set is reprersented with a bubble which is coloured based on the EGSEA ranking (in ranking plots ) or gene set regulation direction (in directional plots) and sized based on the gene set cardinality (in ranking plots) or EGSEA Significance score (in directional plots). Since the EGSEA "Significance Score" is proportional to the p-value and the absolute fold changes, it could be useful to highlight gene sets that have high Significance scores. The blue labels on the summary plot indicate gene sets that do not appear in the top 10 list of gene sets based on the "sort.by" argument (black labels) yet they appear in the top 5 list of gene sets based on the EGSEA "Significance Score". If two contrasts are provided, the rank is calculated based on the "comparison" analysis results and the "Significance Score" is calculated as the mean.
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570
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571 **Pathways page**
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572
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573 The Pathways page shows the KEGG pathways for the gene sets that are presented in the Stats Table of a KEGG gene set collection. The gene fold changes are overlaid on the pathway maps and coloured based on the gene regulation direction: blue for down-regulation and red for up-regulation. Note that this page only appears if a KEGG gene set collection is used in the EGSEA analysis.
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574
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575 **GO Graphs page**
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576
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577 The GO Graphs page shows the Gene Ontology graphs for top 5 GO terms in each of three GO categories: Biological Processes (BP), Molecular Functions (MF), and Cellular Components (CC). Nodes are coloured based on the default sort.by score where red indicates high significance and yellow indicates low significance. Note that this page only appears if a Gene Ontology gene set collection is used, i.e., for the c5 collection from MSigDB or the gsdbgo collection from GeneSetDB.
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578
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579 **Interpret Results link**
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580
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581 The Interpret Results hyperlink in the EGSEA report allows the user to download the fold changes and limma analysis results and thus improve the interpretation of the results.
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582
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583 .. class:: warningmark
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584
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585 Note that the running time of this tool depends on a number of things, including the number of samples and contrasts provided as input, and also the number of gene set testing methods and gene set collections chosen. For example, the `egsea.cnt example`_ in the EGSEA vignette was conducted with 8 samples and 2 contrasts, using the KEGG Signaling and Disease pathways, and 7 of the 12 gene set testing methods, on a MacBook Pro machine that had a 2.8 GHz Intel Core i7 CPU and 16 GB of RAM. The execution time took 145.5 seconds using 16 threads.
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586
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587 .. _egsea.cnt example: https://bioconductor.org/packages/release/bioc/vignettes/EGSEA/inst/doc/EGSEA.pdf
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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588
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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589 -----
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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590
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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591 **More Information**
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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592
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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593 **MSigDB Gene Set Colletions**
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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594
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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595 The MSigDB_ gene sets are divided into 8 major collections:
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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596
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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597 * **H: hallmark gene sets** are coherently expressed signatures derived by aggregating many MSigDB gene sets to represent well-defined biological states or processes.
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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598 * **C1: positional gene sets** for each human chromosome and cytogenetic band.
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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599 * **C2: curated gene sets** are from online pathway databases, publications in PubMed, and knowledge of domain experts.
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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600 * **C3: motif gene sets** are based on conserved cis-regulatory motifs from a comparative analysis of the human, mouse, rat, and dog genomes.
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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601 * **C4: computational gene sets** are defined by mining large collections of cancer-oriented microarray data.
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
602 * **C5: GO gene sets** consist of genes annotated by the same GO terms.
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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603 * **C6: oncogenic gene sets** are defined directly from microarray gene expression data from cancer gene perturbations.
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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604 * **C7: immunologic gene sets** are defined directly from microarray gene expression data from immunologic studies.
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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605
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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606 -----
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
607
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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608 **GeneSetDB Gene Set Colletions**
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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609
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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610 GeneSetDB_ gene sets were obtained from `multiple source databases`_ (shown below) and were classified into five subclasses based on the database content: Pathway, Disease/Phenotype, Drug/Chemical, Genes Regulation and Gene Ontology.
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
611
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
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612 **Pathway**
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
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613
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
614 * Biocarta
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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615 * EHMN (Edinburgh Human Metabolic Network)
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
616 * HumnCyc
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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617 * INOH (Integrating Network Objects with Hierarchies)
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
618 * NetPath
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
619 * PID (Pathway Interaction Database)
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
620 * Reactome
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
621 * Wikipathways
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
622
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
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623 **Disease/Phenotype**
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
624
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
625 * CancerGenes
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
626 * KEGG Disease
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
627 * HPO (Human Phenotype Ontology)
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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628 * MethCancerDB
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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629 * MethyCancer
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
630 * MPO (Mammalian Phenotype Ontology)
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
631 * SIDER (SIDe Effect Resource)
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iuc
parents:
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632
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
633 **Drug/Chemical**
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iuc
parents:
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634
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
635 * CTD (Comparative Toxicogenomics Database)
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
636 * DrugBank
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
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637 * MATADOR (Manually Annotated Targets and Drugs Online Resource)
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
638 * SMPDB (Small Molecular Pathway DataBase)
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
639 * STITCH (Search Tool for Interactions of Chemicals)
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
640 * T3DB (Toxin and Toxin Target Database)
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
641
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
642 **Gene Regulation**
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
643
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
644 * MicroCosm Targets
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
645 * miRTarBase
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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diff changeset
646 * TFactS
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
647 * Rel/NF-kappaB target genes
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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648
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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649 **Gene Ontology**
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
650
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
diff changeset
651 * Gene Ontology
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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652
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653 -----
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
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654
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655 **KEGG Pathways**
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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656
1
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diff changeset
657 Obtained by EGSEAdata from the GAGE_ Bioconductor package using the gage function kegg.gsets(). The Pathview_ Bioconductor package is used to visualize the expression data mapped onto the KEGG pathway graphs. Pathview has a GPLv3 licence which means users are required to formally cite the original `Pathview paper`_ (not just mention it) in publications or products. GAGE/Pathview divide the KEGG pathways into 3 categories: Signaling, Metabolism and Disease, listed in this file at the `Pathview website here`_. You can choose if you want to download the most recent KEGG pathways by selecting the ``Download KEGG pathways`` option in the tool form above. Note that downloading the most recent pathways may affect reproducibility as you can't choose what versions of pathways to use.
0
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658
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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659 **Signaling**
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
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660
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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diff changeset
661 * Genetic Information Processing
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
iuc
parents:
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662 * Environmental Information Processing
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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663 * Cellular Processes
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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664 * Organismal Systems
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665
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666 **Metabolism**
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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667
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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668 * Metabolism
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iuc
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669
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670 **Disease**
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671
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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672 * Human Diseases
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parents:
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673
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674 -----
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parents:
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675
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676 Please cite EGSEA_, MSigDB_, KEGG_ and GeneSetDB_ appropriately if you use them.
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677
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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678 .. _EGSEA: https://www.ncbi.nlm.nih.gov/pubmed/27694195
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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679 .. _Bioconductor package: https://bioconductor.org/packages/release/bioc/html/EGSEA.html
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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680 .. _MSigDB: http://software.broadinstitute.org/gsea/msigdb
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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681 .. _KEGG: http://www.genome.jp/kegg/
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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682 .. _GeneSetDB: http://genesetdb.auckland.ac.nz/haeremai.html
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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683 .. _EGSEA workflow: https://www.bioconductor.org/help/workflows/EGSEA123/
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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684 .. _multiple source databases: http://genesetdb.auckland.ac.nz/sourcedb.html
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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685 .. _GAGE: https://bioconductor.org/packages/release/bioc/html/gage.html
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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686 .. _Pathview: https://bioconductor.org/packages/release/bioc/html/pathview.html
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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687 .. _Pathview paper: https://www.ncbi.nlm.nih.gov/pubmed/23740750
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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688 .. _Pathview website here: https://pathview.uncc.edu/data/khier.tsv
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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689
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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690 ]]></help>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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691 <citations>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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692 <citation type="doi">10.1093/bioinformatics/btw623</citation>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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693 </citations>
a8a083193440 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/egsea commit 7d0c7d850cd56ea3e54d8c03266f719241b20b8b
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694 </tool>