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view abundance_estimates_to_matrix.xml @ 21:400691c87530 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
author | iuc |
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date | Tue, 08 Aug 2023 09:13:04 +0000 |
parents | a009c96c5c18 |
children | ba3720d7e68b |
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<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>for a de novo assembly of RNA-Seq data by Trinity</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools"/> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ #import re #for $entry in $samples: ln -f -s '${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} #if $gene_trans_map: --gene_trans_map '$gene_trans_map' #else: --gene_trans_map 'none' #end if #for $entry in $samples: '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' #end for && mv *.isoform.counts.matrix '$trans_counts' && mv *.isoform.TPM.not_cross_norm '$TPM_no_norm' #if $gene_trans_map: && mv *.gene.counts.matrix '$trans_counts_gene' && mv *.gene.TPM.not_cross_norm '$TPM_no_norm_gene' #end if #if $additional_params.cross_sample_norm == "TMM": && mv *.isoform.TMM.EXPR.matrix '$norm_TMM' #if $gene_trans_map: && mv *.gene.TMM.EXPR.matrix '$norm_TMM_gene' #end if #else if $additional_params.cross_sample_norm == "UpperQuartile": && mv *.isoform.UpperQuartile.EXPR.matrix '$norm_UQ' #if $gene_trans_map: && mv *.gene.UpperQuartile.EXPR.matrix '$norm_UQ_gene' #end if #end if ]]></command> <inputs> <param name="samples" type="data" format="tabular" multiple="true" label="Abundance estimates" help="output(s) from 'Align reads and estimate abundance' tool" /> <param argument="--gene_trans_map" type="data" format="tabular" optional="true" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" help="Only needed for gene level estimates" /> <param type="select" argument="--est_method" label="Abundance estimation method"> <option value="RSEM">RSEM</option> <option value="eXpress">eXpress</option> <option value="salmon">Salmon</option> <option value="kallisto">Kallisto</option> </param> <section name="additional_params" title="Additional Options" expanded="False"> <param type="select" 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 ${on_string}: estimated RNA-Seq fragment isoform counts (raw counts)"/> <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: Matrix of isoform TPM expression values (not cross-sample normalized)"/> <data format="tabular" name="trans_counts_gene" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment gene counts (raw counts)"> <filter>gene_trans_map</filter> </data> <data format="tabular" name="TPM_no_norm_gene" label="${tool.name} on ${on_string}: Matrix of gene TPM expression values (not cross-sample normalized)"> <filter>gene_trans_map</filter> </data> <data format="tabular" name="norm_TMM" label="${tool.name} on ${on_string}: Matrix of TMM-normalized expression values"> <filter>additional_params['cross_sample_norm'] == "TMM"</filter> </data> <data format="tabular" name="norm_UQ" label="${tool.name} on ${on_string}: Matrix of UpperQuartile-normalized expression values"> <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter> </data> <data format="tabular" name="norm_TMM_gene" label="${tool.name} on ${on_string}: Matrix of TMM-normalized expression values (gene)"> <filter>additional_params['cross_sample_norm'] == "TMM" and gene_trans_map</filter> </data> <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: Matrix of UpperQuartile-normalized expression values (gene)"> <filter>additional_params['cross_sample_norm'] == "UpperQuartile" and gene_trans_map</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_TMM"> <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_TMM"> <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_TMM"> <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_UQ"> <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> <test> <param name="samples" ftype="tabular" value="count/kallisto/abundance.tsv.genes,count/kallisto/abundance_B.tsv.genes"/> <param name="est_method" value="kallisto"/> <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_TMM"> <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: https://github.com/trinityrnaseq/trinityrnaseq/wiki ]]> </help> <expand macro="citation" /> </tool>