Mercurial > repos > peter-waltman > ucsc_cluster_tools2
view cluster.tools/heatmap.from.cluster.result.xml @ 6:3d3a8595b981 draft
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author | peter-waltman |
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date | Fri, 01 Mar 2013 19:54:08 -0500 |
parents | 563832f48c08 |
children | a58527c632b7 |
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<tool id="cluster_heatmap" name="Generate Heatmap for Clustering Result" force_history_refresh="True"> <command interpreter="python">heatmap.from.cluster.result.py -d ${dataset1} -s ${cluster_second_direction_cond.cluster_second_direction} #if str($cluster_second_direction_cond.cluster_second_direction) == 'prev': -D ${cluster_second_direction_cond.dataset2} #end if -i ${image_format_cond.image_format} -t ${output_treeview_format} -r ${reverse_rows} -k ${plot_kms_cond.plot_kms} #if str($plot_kms_cond.plot_kms) == 'yes': -C ${dataset1} -S ${plot_kms_cond.survial_data} -M ${plot_kms_cond.mode} -T "${plot_kms_cond.title}" -I none #end if #if str($image_format_cond.image_format) == 'png': -h $report_html -p ${report_html.files_path} #end if #if str($image_format_cond.image_format) == 'pdf': -h $report_pdf -p ${report_pdf.files_path} #end if #if str($treeview_output) != 'None': -o ${treeview_output} #end if </command> <inputs> <param format="rdata" name="dataset1" type="data" label="Clustering Classification" help="Cluster result file from CCPLUS, HAC, or PAM"/> <conditional name="plot_kms_cond"> <param name="plot_kms" type='select' label="Plot Kaplan-Meiers Survival Plot as well (primary clustering ONLY)?" help="NOTE: this only works when the Image Format is PNG. For a PDF of the KM plot, you can use the 'Generate Kaplan-Meiers Plot for Cluster Result' tool"> <option value="yes" >Yes</option> <option value="no" selected='true'>No</option> </param> <when value='yes'> <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)"/> <param name="mode" type="select" display='radio' label="Report Mode" help="Specify the mode to use when performing Log-Rank tests (see help below)"> <option value="all" selected='true' >All</option> <option value="one">One</option> <option value="both">Both</option> </param> <param name="title" type="text" label="Title" value="Report"/> </when> </conditional> <conditional name="cluster_second_direction_cond"> <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)"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> <option value="prev">Previous Cluster Result</option> </param> <when value="prev"> <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"/> </when> </conditional> <conditional name="image_format_cond"> <param name="image_format" type="select" display='radio' label="Image format"> <option value="pdf">PDF</option> <option value="png" selected='true' >PNG (html wrapper)</option> </param> </conditional> <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" > <option value="yes" selected='true' >Yes</option> <option value="no">No</option> </param> <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)" > <option value="yes">Yes</option> <option value="no" selected='true'>No</option> </param> </inputs> <outputs> <data format="html" name="report_html" label="Heatmap from cluster results (HTML)"> <filter>(image_format_cond['image_format']=="png")</filter> </data> <data format="pdf" name="report_pdf" label="Heatmap from cluster results (PDF)"> <filter>(image_format_cond['image_format']=="pdf")</filter> </data> <data format="tgz" name="treeview_output" label="Heatmap from cluster results (tgz of TreeView files)"> <filter>(output_treeview_format)=="yes"</filter> </data> </outputs> <help> .. class:: infomark **Generate Heatmap for Clustering Result** - Tool to generate a heatmap and dendrogram for a clustering result **OUTPUT:** * **Heatmap** in either PDF or PNG format * **TreeView Files** gzip tarball file of the relevant files (OPTIONAL) ---- **Parameters** - **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). - **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. - **Cluster the second dimension?** Specify whether or not to cluster the 2nd dimension of matrix in the cluster result. Choice of: * No * Yes - Generate a default clustering (HAC with Euclidean distance) * Previous Cluster Result - MUST specify a previous clustering result - **IF Cluster the second dimension? is a previous clustering result:** * **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). - **IF Plot Kaplan-Meiers Survival Plot is YES:** * **Clinical Data** Clinical data to use for the Kaplan-Meiers Plot (must be formated - See the "Format Raw TCGA sample IDs") * **Report Mode** Mode to use when performing Log-Rank tests **(MUST SPECIFY A PROPERLY FORMATTED CLINICAL DATA FILE)** . Choice of: * All - All clusters versus each other * One - One cluster versus a meta-cluster composed of the others. Search performed exhaustively. * Both - Perform both all-v-all and and one-v-others test; select the choice of K that gives the best * **Title** - Title to use for Kaplan-Meiers Plot </help> </tool>