view ucsc.cancer.tools/cluster.tools/rdata.2.out.xml @ 0:152f04286b4f draft

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<tool id="rdata_2_out" name="RData cluster result to Text output" force_history_refresh="True">
    <command interpreter="python">rdata.2.out.py
-d $dataset 
-f ${out_format.format}

#if str($out_format.format) == 'cls-only':
-o ${output_cls}
#end if

#if str($out_format.format) == 'newick':
-o ${output_newick}
#end if

#if str($out_format.format) == 'cdt':
#if str($out_format.cdt_sec_dir_data) != "None":
-D ${out_format.cdt_sec_dir_data}
#end if
-o ${output_cdt}
-p ${output_cdt.files_path}
#end if

#if str($out_format.format) == 'tabular':
#if str($out_format.tab_sec_dir_data) != "None":
-D ${out_format.tab_sec_dir_data}
#end if
-o ${output_tab}
-p ${output_tab.files_path}
#end if

</command>
    <inputs>
    	<param name="dataset" type="data" format='rdata' label="Clustering Classification"/>
	<conditional name="out_format" >
	  <param name="format" type="select" label="Select Output Format" >
	    <option value="cls-only" selected='true'>Cluster Assignments Only</option>
	    <option value="newick">Newick</option>
	    <option value="cdt">TreeView (CDT)</option>
	    <option value="tabular">Tab-delimited (all data, ordered by clusters)</option>
	  </param>
	  <when value='cdt'>
	    <param name="cdt_sec_dir_data" type="data" format='rdata' label="Previous Cluster result #2 (secondary result, e.g. rows)" optional="true"/>
	  </when>
	  <when value='tabular'>
	    <param name="tab_sec_dir_data" type="data" format='rdata' label="Previous Cluster result #2 (secondary result, e.g. rows)" optional="true"/>
	  </when>
	</conditional>
    </inputs>
    <outputs>
        <data format="tabular" name="output_cls" label="Cluster Assignments Only (tab-delimited)" >
	  <filter>(out_format['format']=="cls-only")</filter>
	</data>
        <data format="tgz" name="output_cdt" label="CDT File (tgz with CDT and ATR or GTR)" >
	  <filter>(out_format['format']=="cdt")</filter>
	</data>
        <data format="tabular" name="output_newick" label="Newick File" >
	  <filter>(out_format['format']=="newick")</filter>
	</data>
        <data format="tabular" name="output_tab" label="Tab-delimited File" >
	  <filter>(out_format['format']=="tabular")</filter>
	</data>
    </outputs>
<help>
.. class:: infomark
     
**Convert RData file with cluster assignments and data to text (see below for text file options)** - Tool to convert a cluster assignment in tab-delimited format into an RData file format that can be read by the other tools in the Cluster-Tools Suite, e.g. The Kaplan-Meier Survival Plotting Tools


**OUTPUT:**  A new CDT file

----

**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).
- **Select Output Format** Choice of the following
         * Cluster Assignments Only (2-column tab-delimited (ID-Cluster pairs)
         * Newick - dendrogram in Newick format
         * TreeView (CDT) - tarbal (tgz file) with requisite files (e.g. cdt, atr, gtr, jtv files)
         * Tab-delimited (all data, ordered by clusters)

- **IF Output Format is either TreeView or Tab-delimited (all data, ordered by clusters)**
         * **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).


</help>
</tool>