diff cluster.tools/rdata.2.out.xml @ 0:0decf3fd54bc draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cluster.tools/rdata.2.out.xml	Thu Feb 28 01:45:39 2013 -0500
@@ -0,0 +1,86 @@
+<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>