Mercurial > repos > iuc > trinity
diff samples_qccheck.xml @ 2:de0af39266ef draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 77385ec02b79f527348aff01bd83a019e30f5f45
author | iuc |
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date | Mon, 25 Apr 2016 10:02:37 -0400 |
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children | e4a9e0798360 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samples_qccheck.xml Mon Apr 25 10:02:37 2016 -0400 @@ -0,0 +1,114 @@ +<tool id="samples_qccheck" name="RNASeq samples quality check" version="2.1.1"> + <description>for transcript quantification</description> + <requirements> + <requirement type="package" version="2.1.1">trinity</requirement> + <requirement type="package" version="2.30.0">bioconductor-biobase</requirement> + <requirement type="package" version="2.2.2">bioconductor-qvalue</requirement> + </requirements> + <stdio> + <exit_code range="1:"/> + </stdio> + <command><![CDATA[ + + ln -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" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/> + <param format="tabular" name="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" visible="true" /> + </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.minCol10.minRow10.CPM.log2.principal_components.pdf" compare="sim_size" delta="100" file="count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.principal_components.pdf"/> + <element name="input.matrix.minCol10.minRow10.CPM.log2.sample_cor_matrix.pdf" compare="sim_size" delta="100" file="count/qcheck/matrix.counts.matrix.minCol10.minRow10.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 +=========== ================ + +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> + + <citations> + <citation type="doi">doi:10.1038/nbt.1883</citation> + </citations> +</tool> +