diff define_clusters_by_cutting_tree.xml @ 0:acff96adcbec draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit b9a2194247d728ef4d5a3c5511aa6ea63e9b2bcb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/define_clusters_by_cutting_tree.xml	Tue Dec 13 14:43:00 2016 -0500
@@ -0,0 +1,92 @@
+<tool id="trinity_define_clusters_by_cutting_tree" name="Partition genes into expression clusters" version="@WRAPPER_VERSION@.0">
+    <description>after differential expression analysis using a Trinity assembly</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements">
+        <requirement type="package" version="2.30.0">bioconductor-biobase</requirement>
+    </expand>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+
+        define_clusters_by_cutting_tree.pl
+
+        -R '${rdata}'
+
+        #if str( $method.method_selector ) == "--Ptree":
+            --Ptree ${method.ptree}
+        #else
+            #if str( $method.method_selector ) == "--Ktree":
+                --Ktree ${method.ktree}
+            #else
+                -K ${method.k}
+            #end if
+        #end if
+
+        $additional_params.column_ordering
+
+        &&
+        mv *.clusters_fixed_*/* .
+
+    ]]></command>
+    <inputs>
+        <param format="RData" name="rdata" argument="-R" type="data" label="RData file" help="RData file produced by 'Extract and cluster differentially expressed transcripts from a Trinity assembly' tool"/>
+        <conditional name="method">
+            <param name="method_selector" type="select" label="Method for partitioning genes into clusters">
+                <option value="--Ptree">Cut tree based on x percent of max(height) of tree</option>
+                <option value="--Ktree">Cut tree into K clusters</option>
+                <option value="-K">Define K clusters via k-means algorithm</option>
+            </param>
+            <when value="--Ptree">
+                <param name="ptree" type="float" argument="--Ptree" value="20" label="Cut tree based on this percent of max(height) of tree" help="Give a percent value"/>
+            </when>
+            <when value="--Ktree">
+                <param name="ktree" type="integer" argument="--Ktree" value="2" label="Cut tree into K clusters "/>
+            </when>
+            <when value="-K">
+                <param name="k" type="integer" argument="-K" value="2" label="Define K clusters via k-means algorithm" help="This does not leverage the already hierarchically clustered genes, and instead uses a least-sum-of-squares method to define exactly k gene clusters."/>
+            </when>
+        </conditional> 
+        <section name="additional_params" title="Additional Options" expanded="False">
+            <param name="column_ordering" type="select" label="Column ordering in expression matrices" argument="--no_column_reordering / --lexical_column_ordering">
+                <option value="">Order based on sample clustering</option>
+                <option value="--no_column_reordering">No reordering based on sample clustering</option>
+                <option value="--lexical_column_ordering">Reorder column names according to lexical ordering</option>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="expression_matrices" type="list" label="${tool.name} on ${on_string}: expression matrices for each cluster">
+            <discover_datasets pattern="(?P&lt;name&gt;.+_log2_medianCentered_fpkm\.matrix)$" ext="tabular" />
+        </collection>
+        <data format="pdf" name="cluster_plots" label="${tool.name} on ${on_string}: cluster plots" from_work_dir="my_cluster_plots.pdf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="rdata" value="count/analyze_diff_expr/results.matrix.RData"/>
+            <conditional name="method">
+                <param name="method_selector" value="--Ptree"/>
+                <param name="ptree" value="60"/>
+            </conditional>
+            <output_collection name="expression_matrices">
+                <element name="subcluster_1_log2_medianCentered_fpkm.matrix" compare="sim_size" file="count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix"/>
+                <element name="subcluster_2_log2_medianCentered_fpkm.matrix" compare="sim_size" file="count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix"/>
+            </output_collection>
+            <output name="rdata" delta="100" compare="sim_size" file="count/define_clusters_by_cutting_tree/my_cluster_plots.pdf"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
+This tool partitions the differentially expressed genes into gene clusters with similar expression patterns by one of several available methods, once differential expression analyses have been runned. It is a companion tool for the tool 'Extract and cluster differentially expressed transcripts from a Trinity assembly'.
+
+**Inputs**
+
+This tool uses the RData file produced by 'Extract and cluster differentially expressed transcripts from a Trinity assembly' tool.
+
+.. _Trinity: http://trinityrnaseq.github.io
+]]>
+    </help>
+
+    <expand macro="citation" />
+</tool>