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view abundance_estimates_to_matrix.xml @ 2:5a97898c6e63 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c
author | iuc |
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date | Mon, 21 Nov 2016 09:20:39 -0500 |
parents | fba77b1f69b4 |
children | 8b5039bdf1f6 |
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<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.1"> <description>for a de novo assembly of RNA-Seq data by Trinity</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> <requirement type="package" version="3.14.0">bioconductor-edger</requirement> <requirement type="package" version="0.7.2">salmon</requirement> </expand> <expand macro="stdio"/> <command><![CDATA[ #import re #for $entry in $samples: ln -s '${entry}' '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' && #end for abundance_estimates_to_matrix.pl --est_method ${est_method} --cross_sample_norm ${additional_params.cross_sample_norm} #for $entry in $samples: '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' #end for ]]></command> <inputs> <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" /> <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> <option value="RSEM">RSEM</option> <option value="eXpress">eXpress</option> <option value="salmon">Salmon</option> </param> <section name="additional_params" title="Additional Options" expanded="False"> <param type="select" name="cross_sample_norm" argument="--cross_sample_norm" label="Cross sample normalization"> <option value="TMM">TMM</option> <option value="UpperQuartile">UpperQuartile</option> <option value="none">None</option> </param> </section> </inputs> <outputs> <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment counts (raw counts)" from_work_dir="matrix.counts.matrix"/> <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of TPM expression values (not cross-sample normalized)" from_work_dir="matrix.TPM.not_cross_norm"/> <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values" from_work_dir="matrix.TMM.EXPR.matrix"> <filter>additional_params['cross_sample_norm'] == "TMM"</filter> </data> <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values" from_work_dir="matrix.UpperQuartile.EXPR.matrix"> <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter> </data> </outputs> <tests> <test> <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> <param name="est_method" value="RSEM"/> <param name="cross_sample_norm" value="TMM"/> <output name="trans_counts"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> <output name="TPM_no_norm"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> <output name="norm"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> </test> <test> <param name="samples" ftype="tabular" value="count/rsem_bowtie2/sample_A,count/rsem_bowtie2/sample_B"/> <param name="est_method" value="RSEM"/> <param name="cross_sample_norm" value="TMM"/> <output name="trans_counts"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> <output name="TPM_no_norm"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> <output name="norm"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> </test> <test> <param name="samples" ftype="tabular" value="count/express_bowtie/sample_A,count/express_bowtie/sample_B"/> <param name="est_method" value="eXpress"/> <param name="cross_sample_norm" value="TMM"/> <output name="trans_counts"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> <output name="TPM_no_norm"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> <output name="norm"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> </test> <test> <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> <param name="est_method" value="RSEM"/> <param name="cross_sample_norm" value="UpperQuartile"/> <output name="trans_counts"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> <output name="TPM_no_norm"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> <output name="norm"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> </assert_contents> </output> </test> <test> <param name="samples" ftype="tabular" value="count/rsem_bowtie/sample_A,count/rsem_bowtie/sample_B"/> <param name="est_method" value="RSEM"/> <param name="cross_sample_norm" value="none"/> <output name="trans_counts"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> <output name="TPM_no_norm"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> </test> <test> <param name="samples" ftype="tabular" value="count/salmon/sample_A,count/salmon/sample_B"/> <param name="est_method" value="salmon"/> <param name="cross_sample_norm" value="none"/> <output name="trans_counts"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> <output name="TPM_no_norm"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> </assert_contents> </output> </test> </tests> <help> <![CDATA[ Trinity_ assembles transcript sequences from Illumina RNA-Seq data. This tool will combine abundance estimations (produced by 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool) from multiple samples into a single tabular file. This matrix can then be used by 'RNASeq samples quality check for transcript quantification' and 'Differential Expression Analysis using a Trinity assembly' tools. **Inputs** It takes as input multiple results from 'Align reads and estimate abundance on a de novo assembly of RNA-Seq data' tool/ Each sample must have a name, that should be used in subsequent tools. **Output** This tool will produce a single matrix file. More details on this page: .. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-Transcript-Quantification .. _Trinity: http://trinityrnaseq.github.io ]]> </help> <expand macro="citation" /> </tool>