Mercurial > repos > peter-waltman > ucsc_cluster_tools
comparison cluster.tools/heatmap.from.cluster.result.xml @ 2:b442996b66ae draft
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author | peter-waltman |
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date | Wed, 27 Feb 2013 20:17:04 -0500 |
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1:e25d2bece0a2 | 2:b442996b66ae |
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1 <tool id="cluster_heatmap" name="Generate Heatmap for Clustering Result" force_history_refresh="True"> | |
2 <command interpreter="python">heatmap.from.cluster.result.py | |
3 -d ${dataset1} | |
4 -s ${cluster_second_direction_cond.cluster_second_direction} | |
5 | |
6 #if str($cluster_second_direction_cond.cluster_second_direction) == 'prev': | |
7 -D ${cluster_second_direction_cond.dataset2} | |
8 #end if | |
9 -i ${image_format_cond.image_format} | |
10 -t ${output_treeview_format} | |
11 -r ${reverse_rows} | |
12 #if str($plot_kms_cond.plot_kms) == 'yes': | |
13 -C ${dataset1} | |
14 -S ${plot_kms_cond.survial_data} | |
15 -M ${plot_kms_cond.mode} | |
16 -T "${plot_kms_cond.title}" | |
17 -I none | |
18 #end if | |
19 | |
20 #if str($image_format_cond.image_format) == 'png': | |
21 -h $report_html | |
22 -p ${report_html.files_path} | |
23 #end if | |
24 #if str($image_format_cond.image_format) == 'pdf': | |
25 -h $report_pdf | |
26 -p ${report_pdf.files_path} | |
27 #end if | |
28 #if str($treeview_output) != 'None': | |
29 -o ${treeview_output} | |
30 #end if | |
31 | |
32 </command> | |
33 <inputs> | |
34 <param format="rdata" name="dataset1" type="data" label="Clustering Classification" help="Cluster result file from CCPLUS, HAC, or PAM"/> | |
35 <conditional name="plot_kms_cond"> | |
36 <param name="plot_kms" type='select' label="Plot Kaplan-Meiers Survival Plot as well (primary clustering ONLY)?" > | |
37 <option value="no" selected='true'>No</option> | |
38 <option value="yes" >Yes</option> | |
39 </param> | |
40 <when value='yes'> | |
41 <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)"/> | |
42 <param name="mode" type="select" display='radio' label="Report Mode" help="Specify the mode to use when performing Log-Rank tests (see help below)"> | |
43 <option value="all" selected='true' >All</option> | |
44 <option value="one">One</option> | |
45 <option value="both">Both</option> | |
46 </param> | |
47 <param name="title" type="text" label="Title" value="Report"/> | |
48 </when> | |
49 </conditional> | |
50 <conditional name="cluster_second_direction_cond"> | |
51 <param name="cluster_second_direction" type="select" label="Cluster the second dimension? (e.g. rows if this is a sample cluster)" help="Cluster the 2nd dimension of matrix in the cluster result (see help below)"> | |
52 <option value="no" selected="true">No</option> | |
53 <option value="yes">Yes</option> | |
54 <option value="prev">Previous Cluster Result</option> | |
55 </param> | |
56 <when value="prev"> | |
57 <param format="rdata" name="dataset2" type="data" label="Previous Cluster result #2 (secondary result, e.g. rows)" help="Cluster result file from CCPLUS, HAC, or PAM"/> | |
58 </when> | |
59 </conditional> | |
60 <conditional name="image_format_cond"> | |
61 <param name="image_format" type="select" display='radio' label="Image format"> | |
62 <option value="pdf">PDF</option> | |
63 <option value="png" selected='true' >PNG (html wrapper)</option> | |
64 </param> | |
65 </conditional> | |
66 <param name="output_treeview_format" type='select' display="radio" label="Output in TreeView format as well?" help="Specify whether or not to produce files for TreeView" > | |
67 <option value="no">No</option> | |
68 <option value="yes" selected='true' >Yes</option> | |
69 </param> | |
70 <param name="reverse_rows" type='select' display="radio" label="Reverse Row-order (to make consistent w\TreeView Display)?" help="Specify whether or not to reverse Row-order (to make the heatmap consistent with output from TreeView (reversed otherwise)" > | |
71 <option value="no" selected='true'>No</option> | |
72 <option value="yes">Yes</option> | |
73 </param> | |
74 </inputs> | |
75 <outputs> | |
76 <data format="html" name="report_html" label="Heatmap from cluster results (HTML)"> | |
77 <filter>(image_format_cond['image_format']=="png")</filter> | |
78 </data> | |
79 <data format="pdf" name="report_pdf" label="Heatmap from cluster results (PDF)"> | |
80 <filter>(image_format_cond['image_format']=="pdf")</filter> | |
81 </data> | |
82 <data format="tgz" name="treeview_output" label="Heatmap from cluster results (tgz of TreeView files)"> | |
83 <filter>(output_treeview_format)=="yes"</filter> | |
84 </data> | |
85 </outputs> | |
86 <help> | |
87 .. class:: infomark | |
88 | |
89 **Generate Heatmap for Clustering Result** - Tool to generate a heatmap and dendrogram for a clustering result | |
90 | |
91 **OUTPUT:** | |
92 * **Heatmap** in either PDF or PNG format | |
93 * **TreeView Files** gzip tarball file of the relevant files (OPTIONAL) | |
94 | |
95 ---- | |
96 | |
97 **Parameters** | |
98 | |
99 - **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). | |
100 | |
101 - **Plot Kaplan-Meiers Survival Plot as well (primary clustering ONLY)?** Specify whether or not to also plot a Kaplan-Meiers Surivial Plot. **NOTE*, the cluster results must be a **SAMPLE** cluster. | |
102 | |
103 - **Cluster the second dimension?** Specify whether or not to cluster the 2nd dimension of matrix in the cluster result. Choice of: | |
104 * No | |
105 * Yes - Generate a default clustering (HAC with Euclidean distance) | |
106 * Previous Cluster Result - MUST specify a previous clustering result | |
107 | |
108 - **IF Cluster the second dimension? is a previous clustering result:** | |
109 * **Previous Cluster result #2** Specify the clustering classification for the 2nd dimension (RData file format - use the 'Convert tab-delimited Cluster Assignments to RData" tool to convert assignments in tab-delimited format). | |
110 | |
111 - **IF Plot Kaplan-Meiers Survival Plot is YES:** | |
112 * **Clinical Data** Clinical data to use for the Kaplan-Meiers Plot (must be formated - See the "Format Raw TCGA sample IDs") | |
113 | |
114 * **Report Mode** Mode to use when performing Log-Rank tests **(MUST SPECIFY A PROPERLY FORMATTED CLINICAL DATA FILE)** . Choice of: | |
115 | |
116 * All - All clusters versus each other | |
117 * One - One cluster versus a meta-cluster composed of the others. Search performed exhaustively. | |
118 * Both - Perform both all-v-all and and one-v-others test; select the choice of K that gives the best | |
119 | |
120 * **Title** - Title to use for Kaplan-Meiers Plot | |
121 | |
122 | |
123 </help> | |
124 </tool> |