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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
author | iuc |
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date | Mon, 01 Aug 2016 14:43:38 -0400 |
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children | 18213f29e0b9 |
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<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.0"> <description>using a Trinity assembly</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 --> <requirement type="package" version="1.10.0">deseq2</requirement> <requirement type="package" version="3.14.0">bioconductor-edger</requirement> <requirement type="package" version="3.28.10">bioconductor-limma</requirement> <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement> </expand> <expand macro="stdio"/> <command><![CDATA[ ln -s "${matrix}" "input.matrix" && run_DE_analysis.pl --matrix "input.matrix" --samples_file "${samples}" --method ${method_choice.method} #if $method_choice.method == "edgeR": --dispersion ${method_choice.edger_dispersion} #end if #if $method_choice.method == "ROTS": --ROTS_B ${method_choice.rots_b} --ROTS_K ${method_choice.rots_k} #end if --min_rowSum_counts ${additional_params.min_rowSum_counts} #if $additional_params.reference_sample: --reference_sample ${additional_params.reference_sample} #end if #if $additional_params.contrasts: --contrasts ${additional_params.contrasts} #end if --output results ]]></command> <inputs> <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/> <param format="tabular" name="samples" argument="--samples_file" type="data" label="Sample description" help="file describing samples and replicates"/> <conditional name="method_choice"> <param type="select" name="method" argument="--method" label="Differential analysis method"> <option value="edgeR">edgeR</option> <option value="DESeq2">DESeq2</option> <option value="voom">voom</option> <option value="ROTS">ROTS</option> </param> <when value="edgeR"> <param name="edger_dispersion" argument="--dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" /> </when> <when value="ROTS"> <param name="rots_b" argument="--ROTS_B" type="integer" value="500" label="number of bootstraps and permutation resampling" /> <param name="rots_k" argument="--ROTS_K" type="integer" value="5000" label="largest top genes size" /> </when> <when value="voom"> </when> <when value="DESeq2"> </when> </conditional> <section name="additional_params" title="Additional Options" expanded="False"> <param name="min_rowSum_counts" argument="--min_rowSum_counts" type="integer" value="2" label="Minimum count" help="Only those rows of matrix meeting requirement will be tested"/> <param name="reference_sample" argument="--reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/> <param format="tabular" name="contrasts" argument="--contrasts" optional="true" type="data" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/> </section> </inputs> <outputs> <collection name="DE_results" type="list" label="Differential expression results on ${on_string}"> <discover_datasets pattern="(?P<name>.+)\.DE_results$" ext="tabular" directory="results" /> </collection> <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}"> <discover_datasets pattern="(?P<name>.+)\.pdf$" ext="pdf" directory="results" /> </collection> </outputs> <tests> <test> <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> <param name="samples" value="count/samples.txt"/> <param name="method" value="DESeq2"/> <output_collection name="DE_results"> <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results"/> <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results"/> <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results"/> </output_collection> <output_collection name="PDF_results"> <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf"/> <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/> <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/> </output_collection> </test> <test> <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> <param name="samples" value="count/samples.txt"/> <param name="method" value="edgeR"/> <output_collection name="DE_results"> <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results"/> <element name="input.matrix.wt_37_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results"/> <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results"/> </output_collection> <output_collection name="PDF_results"> <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf"/> <element name="input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf"/> <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf"/> </output_collection> </test> <test> <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> <param name="samples" value="count/samples.txt"/> <param name="method" value="voom"/> <output_collection name="DE_results"> <element name="input.matrix.wt_37_vs_wt_GSNO.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results"/> <element name="input.matrix.wt_37_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results"/> <element name="input.matrix.wt_GSNO_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results"/> </output_collection> <output_collection name="PDF_results"> <element name="input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf"/> <element name="input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf"/> <element name="input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf"/> </output_collection> </test> </tests> <help> <![CDATA[ Trinity_ assembles transcript sequences from Illumina RNA-Seq data. This tool performs differential expression analyses on a transcriptome assembled with Trinity. **Inputs** This tool uses the matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool. You must describe your samples and replicates with a tabular file looking like this: =========== ================ ConditionA CondA_replicate1 ----------- ---------------- ConditionA CondA_replicate2 ----------- ---------------- ConditionB CondB_replicate1 ----------- ---------------- ConditionB CondB_replicate2 ----------- ---------------- ConditionC CondC_replicate1 ----------- ---------------- ConditionC CondC_replicate2 ----------- ---------------- ConditionC CondC_replicate3 =========== ================ It will probably be the same file as used in the tool 'RNASeq samples quality check for transcript quantification'. The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'. .. _Trinity: http://trinityrnaseq.github.io ]]> </help> <expand macro="citation" /> </tool>