Mercurial > repos > peter-waltman > ucsc_cluster_tools
comparison cluster.tools/gen.survival.curves.xml @ 2:b442996b66ae draft
Uploaded
author | peter-waltman |
---|---|
date | Wed, 27 Feb 2013 20:17:04 -0500 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
1:e25d2bece0a2 | 2:b442996b66ae |
---|---|
1 <tool id="gen_survival_curve" name="Generate Kaplan-Meiers Plot for Cluster Result" force_history_refresh="True"> | |
2 <command interpreter="python">gen.survival.curves.py | |
3 -C ${cluster_cls} | |
4 -S ${survial_data} | |
5 -M ${mode} | |
6 -T "${title}" | |
7 -I ${image_format_cond.image_format} | |
8 #if str($image_format_cond.image_format) == 'png': | |
9 -O $report_png | |
10 #end if | |
11 #if str($image_format_cond.image_format) == 'pdf': | |
12 -O $report_pdf | |
13 #end if | |
14 </command> | |
15 <inputs> | |
16 <param name="cluster_cls" type="data" format="rdata" label="Clustering Classification" help="Specify the clustering classification (must be RData file, see help)"/> | |
17 <param name="survial_data" type="data" format="tabular" label="Clinical Data" help="Specify the clinical data to use for the Kaplan-Meiers Plot (see help)"/> | |
18 <param name="mode" type="select" display='radio' label="Report Mode" help="Specify the mode to use when performing Log-Rank tests"> | |
19 <option value="all" selected='true' >All</option> | |
20 <option value="one">One</option> | |
21 <option value="both">Both</option> | |
22 </param> | |
23 <conditional name="image_format_cond"> | |
24 <param name="image_format" type="select" display='radio' label="Image format" help=""> | |
25 <option value="pdf">PDF</option> | |
26 <option value="png" selected='true' >PNG (html wrapper)</option> | |
27 </param> | |
28 </conditional> | |
29 | |
30 <param name="title" type="text" label="Title" value="Report" help="Specify title to use in Kaplan-Meiers Plot"/> | |
31 </inputs> | |
32 <outputs> | |
33 <data format="png" name="report_png" label="Kaplan-Meier Survival Plot (PNG)"> | |
34 <filter>(image_format_cond['image_format']=="png")</filter> | |
35 </data> | |
36 <data format="pdf" name="report_pdf" label="Kaplan-Meier Survival Plot (PDF)"> | |
37 <filter>(image_format_cond['image_format']=="pdf")</filter> | |
38 </data> | |
39 </outputs> | |
40 <help> | |
41 .. class:: infomark | |
42 | |
43 **Generate a Kaplan-Meiers Plot for a given cluster result** | |
44 | |
45 ---- | |
46 | |
47 **Parameters** | |
48 | |
49 - **Clustering Classification** Specify the clustering classification (RData file format - use the 'Convert tab-delimited Cluster Assignments to RData" tool to convert assignments in tab-delimited format). | |
50 | |
51 - **Clinical Data** Clinical data to use for the Kaplan-Meiers Plot (must be formated - See the "Format Raw TCGA sample IDs") | |
52 | |
53 - **Report Mode** Mode to use when performing Log-Rank tests **(MUST SPECIFY A PROPERLY FORMATTED CLINICAL DATA FILE)** . Choice of: | |
54 | |
55 * All - All clusters versus each other | |
56 * One - One cluster versus a meta-cluster composed of the others. Search performed exhaustively. | |
57 * Both - Perform both all-v-all and and one-v-others test; select the choice of K that gives the best | |
58 | |
59 - **Title** - Title to use for Kaplan-Meiers Plot | |
60 | |
61 </help> | |
62 </tool> |