Mercurial > repos > proteore > proteore_clusterprofiler

comparison cluster_profiler.xml @ 6:5e16cec55146 draft

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planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
author proteore
date Thu, 29 Mar 2018 11:43:28 -0400
parents 8a91f58782df
children 4609346d8108
comparison
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5:8a91f58782df 6:5e16cec55146
34 34
35 #if $ego.go_enrich == "true" 35 #if $ego.go_enrich == "true"
36 --go_enrich="true" 36 --go_enrich="true"
37 --pval_cutoff="$ego.pval" 37 --pval_cutoff="$ego.pval"
38 --qval_cutoff="$ego.qval" 38 --qval_cutoff="$ego.qval"
39 #if $ego.universe.universe_option == "true"
40 #if $ego.universe.universe_input.universe_ids == "text"
41 --universe_type="text"
42 --universe="$ego.universe.universe_input.txt"
43 #else
44 --universe_type="file"
45 --universe="$ego.universe.universe_input.file"
46 --uncol="$ego.universe.universe_input.ncol"
47 --uheader="$ego.universe.universe_input.header"
48 #end if
49 --universe_id_type="$ego.universe.universe_idti.universe_idtypein"
50 #end if
39 #else 51 #else
40 --go_enrich="false" 52 --go_enrich="false"
41 #end if 53 #end if
42 54
43 --onto_opt="$ontology" 55 --onto_opt="$ontology"
74 <option value="Entrez">Entrez Gene ID</option> 86 <option value="Entrez">Entrez Gene ID</option>
75 </param> 87 </param>
76 <when value="Uniprot"/> 88 <when value="Uniprot"/>
77 <when value="Entrez"/> 89 <when value="Entrez"/>
78 </conditional> 90 </conditional>
91
79 <param name="species" type="select" label="Select a species" > 92 <param name="species" type="select" label="Select a species" >
80 <option value="human">Human</option> 93 <option value="human">Human</option>
81 <option value="mouse">Mouse</option> 94 <option value="mouse">Mouse</option>
82 <option value="rat">Rat</option> 95 <option value="rat">Rat</option>
83 </param> 96 </param>
95 <conditional name="ego"> 108 <conditional name="ego">
96 <param name="go_enrich" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Do you want to perform GO categories enrichment analysis?"/> 109 <param name="go_enrich" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Do you want to perform GO categories enrichment analysis?"/>
97 <when value="true"> 110 <when value="true">
98 <param name="pval" type="float" value="0.01" label="P-value cut off"/> 111 <param name="pval" type="float" value="0.01" label="P-value cut off"/>
99 <param name="qval" type="float" value="0.05" label="Q-value cut off"/> 112 <param name="qval" type="float" value="0.05" label="Q-value cut off"/>
113 <conditional name="universe" >
114 <param name="universe_option" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Would you like to define your own background IDs?"/>
115 <when value="true">
116 <conditional name="universe_input">
117 <param name="universe_ids" type="select" label="Provide your background IDs list" help="Copy/paste or ID list from a file (e.g. table)" >
118 <option value="text">Copy/paste your background identifiers</option>
119 <option value="file" selected="true">Input file containing your background identifiers</option>
120 </param>
121 <when value="text" >
122 <param name="txt" type="text" label="Copy/paste your background identifiers" help='IDs must be separated by spaces into the form field, for example: P31946 P62258' >
123 <sanitizer>
124 <valid initial="string.printable">
125 <remove value="&apos;"/>
126 </valid>
127 <mapping initial="none">
128 <add source="&apos;" target="__sq__"/>
129 </mapping>
130 </sanitizer>
131 </param>
132 </when>
133 <when value="file" >
134 <param name="file" type="data" format="txt,tabular" label="Choose a file that contains your background IDs list" help="" />
135 <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
136 <param name="ncol" type="text" value="c1" label="The column number of IDs to map" help='For example, fill in "c1" if it is the first column, "c2" if it is the second column and so on' />
137 </when>
138 </conditional>
139 <conditional name="universe_idti" >
140 <param name="universe_idtypein" type="select" label="Select type/source of background identifier of your list" help="Please see example of IDs in help section" >
141 <option value="Uniprot">UniProt accession number</option>
142 <option value="Entrez">Entrez Gene ID</option>
143 </param>
144 <when value="Uniprot"/>
145 <when value="Entrez"/>
146 </conditional>
147 </when>
148 <when value="false"/>
149 </conditional>
100 </when> 150 </when>
101 <when value="false"/> 151 <when value="false"/>
102 </conditional> 152 </conditional>
103 153
104 <param name="ontology" type="select" display="checkboxes" multiple="true" label="Please select GO terms category"> 154 <param name="ontology" type="select" display="checkboxes" multiple="true" label="Please select GO terms category">