Mercurial > repos > iuc > trinity_run_de_analysis
diff run_de_analysis.xml @ 0:1563554bb3f0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
| author | iuc |
|---|---|
| date | Mon, 01 Aug 2016 14:43:38 -0400 |
| parents | |
| children | 18213f29e0b9 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_de_analysis.xml Mon Aug 01 14:43:38 2016 -0400 @@ -0,0 +1,171 @@ +<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>