Mercurial > repos > iuc > trinity_define_clusters_by_cutting_tree
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
author | iuc |
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date | Tue, 13 Dec 2016 14:43:00 -0500 |
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children | cd71eff81169 |
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--- /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 ${on_string}: expression matrices for each cluster"> + <discover_datasets pattern="(?P<name>.+_log2_medianCentered_fpkm\.matrix)$" 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>