Mercurial > repos > trinity_ctat > ctat_abundance_estimation_to_matrix
diff ctat_abundance_estimation_to_matrix.xml @ 0:5eca0c75b178 draft default tip
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author | trinity_ctat |
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date | Tue, 17 Jul 2018 11:47:32 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_abundance_estimation_to_matrix.xml Tue Jul 17 11:47:32 2018 -0400 @@ -0,0 +1,101 @@ +<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>