Mercurial > repos > iuc > trinity_filter_low_expr_transcripts
view filter_low_expr_transcripts.xml @ 0:6821f5ea01d8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
author | iuc |
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date | Mon, 01 Aug 2016 14:44:51 -0400 |
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children | 7246eeaad26d |
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<tool id="trinity_filter_low_expr_transcripts" name="Filter low expression transcripts" version="@WRAPPER_VERSION@.0"> <description>from a Trinity assembly</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ filter_low_expr_transcripts.pl --matrix "$matrix" --transcripts "$assembly" #if $additional_params.gene_map.has_gene_map == "no": --gene_trans_map $additional_params.gene_map.gene_trans_map #else --trinity_mode #end if #if str($min_expr_any): --min_expr_any $min_expr_any #end if #if str($isoform_filter.highest_iso_only) == "yes": --highest_iso_only #else if str($isoform_filter.min_pct_dom_iso): --min_pct_dom_iso $isoform_filter.min_pct_dom_iso #end if > "$filtered" ]]></command> <inputs> <param format="fasta" name="assembly" argument="--transcripts" type="data" label="Trinity assembly"/> <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix"/> <param name="min_expr_any" type="float" argument="--min_expr_any" optional="true" label="Minimum expression level required across any sample"/> <conditional name="isoform_filter"> <param name="highest_iso_only" argument="--highest_iso_only" type="select" label="Only retain the most highly expressed isoform per gene"> <option value="yes">Yes</option> <option value="no" selected="true">No</option> </param> <when value="yes"> </when> <when value="no"> <param name="min_pct_dom_iso" argument="--min_pct_dom_iso" type="integer" optional="true" label="Minimum percent of dominant isoform expression"/> </when> </conditional> <section name="additional_params" title="Additional Options" expanded="False"> <conditional name="gene_map"> <param name="has_gene_map" type="select" label="Trinity assembly?" help="If the transcripts were not assembled by trinity, additional information is needed"> <option value="yes">Yes</option> <option value="no">No</option> </param> <when value="yes"> </when> <when value="no"> <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" /> </when> </conditional> </section> </inputs> <outputs> <data format="tabular" name="filtered" label="${tool.name} on ${on_string}: filtered low expression transcripts"/> </outputs> <tests> <test> <param name="matrix" value="filtered/counts.matrix"/> <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/> <param name="min_expr_any" value="25"/> <output name="filtered" file="filtered/Trinity_filtered_exp.fasta" /> </test> <!-- this option is broken in 2.2.0: https://github.com/trinityrnaseq/trinityrnaseq/issues/129 <test> <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/> <param name="isoform_filter|highest_iso_only" value="yes"/> <output name="filtered" file="filtered/Trinity_filtered_hi_iso.fasta" /> </test--> <test> <param name="matrix" value="filtered/counts.matrix"/> <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/> <param name="isoform_filter|min_pct_dom_iso" value="20"/> <output name="filtered" file="filtered/Trinity_filtered_pct_iso.fasta" /> </test> </tests> <help> Trinity_ assembles transcript sequences from Illumina RNA-Seq data. This tool filters a Trinity assembly using an expression matrix built with "Build expression matrix for a de novo assembly of RNA-Seq data by Trinity" tool. It discards transcripts/isoforms having a low expression level. .. _Trinity: http://trinityrnaseq.github.io </help> <expand macro="citation" /> </tool>