Mercurial > repos > stemcellcommons > scdetools
comparison scde_list_match.xml @ 0:b1d730728d5f default tip
Initial commit.
author | Ilya Sytchev <isytchev@hsph.harvard.edu> |
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date | Mon, 07 Oct 2013 18:54:25 -0400 |
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1 <?xml version="1.0"?> | |
2 <tool id="scde-list-match" name="SCDE ListMatch" version="1.0" hidden="false"> | |
3 <description>match a list against one or more selected reference gene lists</description> | |
4 <version_string>scde --version</version_string> | |
5 | |
6 <command interpreter="perl"> | |
7 scde match --source $source | |
8 --organism $organism | |
9 | |
10 #if str($symbol_type) != "" | |
11 --symbol $symbol_type | |
12 #end if | |
13 | |
14 #if $query.type == "file" | |
15 --file $query.filename | |
16 --column $query.column | |
17 #else | |
18 $query.source | |
19 #end if | |
20 --min-matches $min_matches | |
21 --output $format | |
22 | |
23 #if str($output_html) != "None" | |
24 > $output_html | |
25 #else | |
26 > $output_tab | |
27 #end if | |
28 </command> | |
29 | |
30 <inputs> | |
31 <param name="source" type="select" label="Compare your gene list to"> | |
32 <option value="wikipathways">Wikipathways</option> | |
33 <option value="genesigdb">GeneSigDB</option> | |
34 <option value="msigdb">MSigDB</option> | |
35 <option value="scd">SCDE Repository - Public</option> | |
36 </param> | |
37 | |
38 <param name="organism" type="select" label="Query Organism" help="Which organism did your gene list come from?"> | |
39 <option value="human">Human</option> | |
40 <option value="mouse">Mouse</option> | |
41 </param> | |
42 | |
43 <param name="symbol_type" type="select" label="Query Gene ID Type" help="Select the gene identifier type to search with."> | |
44 <option value="symbol">Gene Symbol</option> | |
45 <option value="ensembl">Ensembl ID</option> | |
46 <option value="entrez">Entrez ID</option> | |
47 </param> | |
48 | |
49 <conditional name="query"> | |
50 <param name="type" type="select" label="Query source" help="You may select a file from your User History or enter a list of genes as text."> | |
51 <option value="file">History File</option> | |
52 <option value="text">Enter Text</option> | |
53 </param> | |
54 | |
55 <when value="file"> | |
56 <param name="filename" format="txt" type="data" label="Query History File" help="Select a file from your History"/> | |
57 <param name="column" type="data_column" data_ref="filename" label="Query File Column Number" help="Column numbers start at 1. Verify that the column number corresponds to the Gene ID Type you specified."/> | |
58 </when> | |
59 | |
60 <when value="text"> | |
61 <param name="source" type="text" area="true" size="5x60" label="Query using Text Entry" help="Paste a list of gene symbols here, separated by a space, tab, new line or a comma."/> | |
62 </when> | |
63 </conditional> | |
64 | |
65 <param name="min_matches" type="select" label="Minimum Number of Matches" help="Select the minimum number of genes that must be matched per reference gene list."> | |
66 <option value="1">1</option> | |
67 <option value="2">2</option> | |
68 <option value="3">3</option> | |
69 <option value="4">4</option> | |
70 <option value="5">5</option> | |
71 </param> | |
72 | |
73 <param name="format" type="select" label="Output Format" help="Select the format for the output file."> | |
74 <option value="html">HTML</option> | |
75 <option value="tab">Tab Delimited</option> | |
76 </param> | |
77 </inputs> | |
78 | |
79 <outputs> | |
80 <data format="html" name="output_html"> | |
81 <filter>format == "html"</filter> | |
82 </data> | |
83 <data format="tabular" name="output_tab"> | |
84 <filter>format == "tab"</filter> | |
85 </data> | |
86 </outputs> | |
87 | |
88 <help> | |
89 **What it does** | |
90 | |
91 This tool compares a list of genes as a query against one or more selected reference lists. | |
92 | |
93 ----- | |
94 | |
95 .. class:: infomark | |
96 | |
97 Please upload your data as a tab-delimited text file. If the column number does not appear as a dropdown menu, make sure the file type is 'Tabular'. | |
98 | |
99 ----- | |
100 | |
101 **Screencast!** | |
102 | |
103 Watch the SCDE ListMatch Screencast_ (right click to open this link in another window). | |
104 | |
105 .. _Screencast: http://discovery.hsci.harvard.edu/screencasts/galaxy.html | |
106 </help> | |
107 </tool> |