Mercurial > repos > iuc > goenrichment
annotate goenrichment.xml @ 0:52964064db8a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
author | iuc |
---|---|
date | Fri, 11 Jan 2019 06:18:35 -0500 |
parents | |
children | 5ace5c7d1a86 |
rev | line source |
---|---|
0
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
1 <tool id="goenrichment" name="GOEnrichment" version="2.0.1"> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
2 <description>performs GO enrichment analysis of a set of gene products</description> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
3 <requirements> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
4 <requirement type="package" version="2.0.1">goenrichment</requirement> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
5 </requirements> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
6 <command detect_errors="exit_code">goenrichment |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
7 --go '${go}' |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
8 --annotation '${annotation}' |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
9 --study '${study}' |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
10 #if str($population) != 'None' |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
11 --population '${population}' |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
12 #end if |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
13 --correction ${correction} |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
14 $summarize |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
15 $singletons |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
16 $relations |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
17 --graph_format $graph |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
18 --cut_off $cutoff |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
19 --mf_result '${mf_result}' |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
20 --bp_result '${bp_result}' |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
21 --cc_result '${cc_result}' |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
22 --mf_graph '${mf_graph}' |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
23 --bp_graph '${bp_graph}' |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
24 --cc_graph '${cc_graph}' |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
25 </command> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
26 <inputs> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
27 <param name="go" type="data" format="obo,owl" label="Gene Ontology File" help="Gene Ontology file in OBO or OWL format (see http://geneontology.org/page/download-ontology)"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
28 <param name="annotation" type="data" format="tabular,txt" label="Gene Product Annotation File" help="Tabular file containing annotations from gene products to GO terms (in GAF or BLAST2GO format, or a simple two-column table)"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
29 <param name="study" type="data" format="txt" label="Study Set File" help="File containing the gene products corresponding to the study set (one per line)"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
30 <param name="population" type="data" format="txt" optional="true" label="Population Set File (Optional)" help="File containing the gene products corresponding to the population set (one per line). If no file is submitted, the population set will be the set of all gene products listed in the annotation file."/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
31 <param name="correction" type="select" label="Multiple Test Correction" help="The multiple test correction method to use (Benjamini-Hochberg is recommended)."> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
32 <option value="Benjamini-Hochberg" selected="true"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
33 <option value="SDA"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
34 <option value="Bonferroni-Holm"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
35 <option value="Sidak"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
36 <option value="Bonferroni"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
37 </param> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
38 <param name="cutoff" type="select" label="P-Value Cut-Off" help="The corrected p-value (or q-value) cut-off to apply for the graph output."> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
39 <option value="1.0"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
40 <option value="0.1"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
41 <option value="0.05"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
42 <option value="0.01" selected="true"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
43 </param> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
44 <param name="graph" type="select" label="Output Graph Format" help="The format of the output graphs (png, svg, or tabular for importing into cytoscape)."> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
45 <option value="png" selected="true"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
46 <option value="svg"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
47 <option value="tabular"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
48 </param> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
49 <param name="summarize" type="boolean" checked="true" truevalue="--summarize_output" falsevalue="" label="Summarize Output" help="Whether to produce a summarized list of GO terms or the full list of those that are statistically significant"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
50 <param name="singletons" type="boolean" checked="true" truevalue="--ignore_singletons" falsevalue="" label="Exclude Singletons" help="Whether to exclude GO terms that are annotated to a single gene product in the study set"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
51 <param name="relations" type="boolean" checked="false" truevalue="--use_all_relations" falsevalue="" label="Use All Relations" help="Whether to infer annotations through 'part_of' and other non-hierarchical relationships, or only through 'is_a' relations"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
52 </inputs> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
53 <outputs> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
54 <data name="mf_result" format="tabular" label="MF Result File"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
55 <data name="bp_result" format="tabular" label="BP Result File"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
56 <data name="cc_result" format="tabular" label="CC Result File"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
57 <data name="mf_graph" format="png" label="MF Graph File"> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
58 <change_format> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
59 <when input="graph" value="svg" format="svg"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
60 <when input="graph" value="tabular" format="tabular"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
61 </change_format> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
62 </data> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
63 <data name="bp_graph" format="png" label="BP Graph File"> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
64 <change_format> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
65 <when input="graph" value="svg" format="svg"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
66 <when input="graph" value="tabular" format="tabular"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
67 </change_format> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
68 </data> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
69 <data name="cc_graph" format="png" label="CC Graph File"> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
70 <change_format> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
71 <when input="graph" value="svg" format="svg"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
72 <when input="graph" value="tabular" format="tabular"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
73 </change_format> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
74 </data> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
75 </outputs> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
76 <tests> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
77 <test> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
78 <param name="go" ftype="obo" value="go.obo"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
79 <param name="annotation" ftype="txt" value="annotations.tab"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
80 <param name="study" ftype="txt" value="study.txt"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
81 <param name="summarize" value="false"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
82 <output name="mf_result" ftype="tabular" file="MF_result.txt" lines_diff="0"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
83 </test> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
84 <test> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
85 <param name="go" ftype="obo" value="go.obo"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
86 <param name="annotation" ftype="txt" value="annotations.tab"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
87 <param name="study" ftype="txt" value="study.txt"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
88 <param name="population" ftype="txt" value="population.txt"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
89 <param name="summarize" value="false"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
90 <output name="mf_result" ftype="tabular" file="MF_result.txt" lines_diff="0"/> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
91 </test> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
92 </tests> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
93 <help> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
94 .. class:: infomark |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
95 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
96 GOEnrichment is a Java application that can be used to analyze gene product sets (e.g., from microarray or RNAseq experiments) for enriched GO terms. |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
97 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
98 ----- |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
99 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
100 .. class:: infomark |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
101 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
102 GOEnrichment requires: |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
103 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
104 - A Gene Ontology file in either OBO or OWL format (see http://geneontology.org/page/download-ontology). |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
105 - A tabular annotation file in GAF (http://geneontology.org/page/download-annotations) format, BLAST2GO format, or a simple two-column table (e.g. from BioMart) with gene product ids in the first column and GO terms in the second one. |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
106 - A list of gene products comprising the study set (a flat text file with one gene product per line). |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
107 - Optionally, a list of gene products comprising the population set (if none is submitted, the population set will be the set of gene products listed in the annotation file). |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
108 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
109 ----- |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
110 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
111 .. class:: infomark |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
112 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
113 GOEnrichment produces a tabular result file and a graph file for each GO type (MF - Molecular Function, BP - Biological Process and CC - Cellular Component): |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
114 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
115 - The result file is a tabular list of all GO terms present in the study set and their respective p-values. |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
116 - The graph file can be either a png image, an svg image, or a text file for importing into cytoscape (together with the result file). |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
117 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
118 ----- |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
119 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
120 .. class:: infomark |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
121 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
122 The graph is colored by p-value: terms with p-value above cut-off appear in white; and the color gets darker as the p-value decreases |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
123 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
124 .. image:: https://github.com/DanFaria/GOEnrichment/raw/master/Scale.png |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
125 :width: 600 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
126 :height: 315 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
127 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
128 (see the scale at https://github.com/DanFaria/GOEnrichment/blob/master/Scale.png). In addition to the name of each GO term, the graph |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
129 shows its frequency in the study set. Dashed edges indicate that one or more intermediate terms were ommited from the graph. |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
130 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
131 ----- |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
132 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
133 .. class:: warningmark |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
134 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
135 Gene products listed in either the study or population set files that are not present in the annotation file will be ignored. |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
136 </help> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
137 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
138 <citations> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
139 <citation type="bibtex"> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
140 @misc{githubgoenrichment, |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
141 author = {Faria, Daniel}, |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
142 year = {2017}, |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
143 title = {GOEnrichment}, |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
144 publisher = {GitHub}, |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
145 journal = {GitHub repository}, |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
146 url = {https://github.com/DanFaria/GOEnrichment}, |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
147 } |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
148 </citation> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
149 </citations> |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
150 |
52964064db8a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goenrichment commit c41d1d8f48da033f601b003d71e0e22345ccdbdb
iuc
parents:
diff
changeset
|
151 </tool> |