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date | Tue, 17 Jul 2018 11:47:32 -0400 |
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<tool id="ctat_abundance_estimation_to_matrix" name="ctat_abundance_estimation_to_matrix" version="1.0.0" profile="17.05"> <description>Join RSEM estimates from multiple samples into a single matrix</description> <requirements> <requirement type="package" version="2.7">python</requirement> <requirement type="package">subprocess32</requirement> <requirement type="package">bzip2</requirement> <requirement type="package" version="1.3.0">rsem</requirement> <requirement type="package" version="3">bioconductor-edger</requirement> <requirement type="package" version="2">bioconductor-qvalue</requirement> <requirement type="package" version="2.6.6">trinity</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ python $__tool_directory__/ctat_abundance_estimation_to_matrix.py #for $q in $RSEM_samples ${q.file} "${q.column_label}" #end for ]]> </command> <inputs> <repeat name="RSEM_samples" title="RSEM abundance estimates for samples"> <param name="file" label="Add file" type="data" format="txt"/> <param name="column_label" label="column label" type="text" /> </repeat> </inputs> <outputs> <data format="tabular" name="counts_matrix" label="${tool.name} on ${on_string}: Counts Matrix" from_work_dir="RSEM.isoform.counts.matrix"/> <data format="tabular" name="tmm_expr_matrix" label="${tool.name} on ${on_string}: TMM EXPR Matrix" from_work_dir="RSEM.isoform.TMM.EXPR.matrix"/> </outputs> <tests> <test> <repeat name="RSEM_samples"> <param name="file" value="Sp_ds.RSEM.genes.results" /> <param name="column_label" value="Sp_ds" /> </repeat> <repeat name="RSEM_samples"> <param name="file" value="Sp_hs.RSEM.genes.results" /> <param name="column_label" value="Sp_hs" /> </repeat> <output name="counts_matrix" > <assert_contents> <has_line_matching expression=".+" /> <has_line line="	Sp_ds	Sp_hs" /> <has_n_columns n="3" /> <has_line_matching expression="TRINITY_DN.+" /> </assert_contents> </output> <output name="tmm_expr_matrix" > <assert_contents> <has_line_matching expression=".+" /> <has_line line="	Sp_ds	Sp_hs" /> <has_n_columns n="3" /> <has_line_matching expression="TRINITY_DN.+" /> </assert_contents> </output> </test> <!-- The following test has not been tested to see if it works. <test> <repeat name="RSEM_samples"> <param name="file" value="Sp_ds.RSEM.isoforms.results" /> <param name="column_label" value="Sp_ds" /> </repeat> <repeat name="RSEM_samples"> <param name="file" value="Sp_hs.RSEM.isoforms.results" /> <param name="column_label" value="Sp_hs" /> </repeat> <output name="counts_matrix" > <assert_contents> <has_line_matching expression=".+" /> </assert_contents> </output> <output name="tmm_expr_matrix" > <assert_contents> <has_line_matching expression=".+" /> </assert_contents> </output> </test> --> </tests> <help> .. class:: infomark This step will join the RSEM-computed gene or isoform fragment counts into a matrix file, which will be used to run edgeR and identify differentially expressed transcripts in next few steps. Execution of this will generate a counts matrix file with a name 'abundance_estimation_to_matrix: counts_matrix'. If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols paper_. .. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki .. _paper: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html </help> <citations> <citation type="doi">10.1038/nbt.1883</citation> </citations> </tool>