Mercurial > repos > devteam > dgidb_annotator

annotate dgidb_annotator.xml @ 0:28d72b995c6b draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 11:29:28 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
1 <tool id="dgidb_annotate" name="Annotate with DGI" version="0.1">
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
2 <description>database info</description>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
3
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
4 <command interpreter="python">
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
5 dgidb_annotator.py
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
6 #if $expert_curated_only:
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
7 -e
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
8 #end if
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
9 #if $print_all:
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
10 -a
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
11 #end if
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
12 -g $gene_name_col
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
13 $input &gt; $output
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
14 </command>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
15 <inputs>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
16 <param name="input" label="Input" type="data" format="tabular"/>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
17 <param name="expert_curated_only" label="Use Only Expert Curated Results" type="boolean"/>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
18 <param name="print_all" label="Print All Rows, including those without Annotation" type="boolean"/>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
19 <param name="gene_name_col" label="Gene Name Column" type="data_column" data_ref="input"/>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
20 </inputs>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
21
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
22 <outputs>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
23 <data name="output" format="tabular"/>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
24 </outputs>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
25
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
26 <stdio>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
27 <regex match=".*" source="both" level="log" description="tool progress"/>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
28 </stdio>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
29
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
30 <tests>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
31 <test>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
32 <param name="input" value="in1.tabular"/>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
33 <param name="expert_curated_only" value="True"/>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
34 <param name="print_all" value="False"/>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
35 <param name="gene_name_col" value="1"/>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
36 <output name="output" file="out1.tabular"/>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
37 </test>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
38 </tests>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
39
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
40 <help>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
41 Annotates a tabular dataset with information from the `Drug-Gene Interations database`__
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
42
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
43 .. __: http://dgidb.genome.wustl.edu/
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
44 </help>
28d72b995c6b planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/dgidb_annotator commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
devteam
parents:
diff changeset
45 </tool>