Mercurial > repos > iuc > trinity_samples_qccheck
view samples_qccheck.xml @ 7:77983b40ffb4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7f726b691ead726864f1b67230cb5d58e16b5f58
author | iuc |
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date | Fri, 15 Dec 2017 08:02:28 -0500 |
parents | 8bec0d476fa0 |
children | 226663afe49c |
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<tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@WRAPPER_VERSION@.0"> <description>for transcript quantification</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="2.34.0">bioconductor-biobase</requirement> <requirement type="package" version="2.6.0">bioconductor-qvalue</requirement> <requirement type="package" version="2.0.6">r-cluster</requirement> </expand> <command detect_errors="aggressive"><![CDATA[ ln -f -s "${matrix}" "input.matrix" && PtR --matrix "input.matrix" --samples "${samples}" --CPM --log2 --compare_replicates && PtR --matrix "input.matrix" --samples "${samples}" --CPM --log2 --sample_cor_matrix && PtR --matrix "input.matrix" --samples "${samples}" --CPM --log2 --prin_comp 3 && mkdir out_pdf && mv *rep_compare.pdf out_pdf/ && mv *sample_cor_matrix.pdf out_pdf/ && mv *principal_components.pdf out_pdf/ ]]></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" type="data" label="Samples description" help="file describing samples and replicates"/> </inputs> <outputs> <collection name="reports" type="list" label="Quality check result files on ${on_string}"> <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" /> </collection> </outputs> <tests> <test> <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> <param name="samples" value="count/samples.txt"/> <output_collection name="reports"> <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/> <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/> <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/> <element name="input.matrix.CPM.log2.principal_components.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.CPM.log2.principal_components.pdf"/> <element name="input.matrix.CPM.log2.sample_cor_matrix.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf"/> </output_collection> </test> </tests> <help> <![CDATA[ Trinity_ assembles transcript sequences from Illumina RNA-Seq data. This tool performs some Quality Checks on a RNASeq experiment, analysing the abundance estimation for different samples using 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 =========== ================ This file can be generated with the 'Describe samples and replicates' tool. 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'. **Output** This tool will produce several PDF files, see the following page for more information: .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/QC-Samples-and-Replicates .. _Trinity: http://trinityrnaseq.github.io ]]> </help> <expand macro="citation" /> </tool>