Mercurial > repos > proteore > proteore_clusterprofiler
comparison cluster_profiler.xml @ 6:5e16cec55146 draft
planemo upload commit 2da0aec067fd35a8ec102ce27ec4bac8f54b1c30-dirty
| author | proteore |
|---|---|
| date | Thu, 29 Mar 2018 11:43:28 -0400 |
| parents | 8a91f58782df |
| children | 4609346d8108 |
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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="'"/> | |
| 126 </valid> | |
| 127 <mapping initial="none"> | |
| 128 <add source="'" 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"> |