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view filter_low_expr_transcripts.xml @ 20:a35cba31d904 draft default tip
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 09:06:58 +0000 |
parents | aa38fa8c5815 |
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<tool id="trinity_filter_low_expr_transcripts" name="Filter low expression transcripts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>from a Trinity assembly</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools"/> <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ #if $additional_params.gene_map.has_gene_map == "yes": get_Trinity_gene_to_trans_map.pl '$assembly' > gene_to_trans.map && #else: ln -f -s '$additional_params.gene_map.gene_trans_map' gene_to_trans.map && #end if filter_low_expr_transcripts.pl --matrix '$matrix' --transcripts '$assembly' --gene_to_trans_map gene_to_trans.map #if str($min_expr_any): --min_expr_any $min_expr_any #end if #if str($isoform_filter.isoform_mode) == "highest_iso_only": --highest_iso_only #else if str($isoform_filter.isoform_mode) == "min_pct_dom_iso": --min_pct_dom_iso $isoform_filter.min_pct_dom_iso #end if > '$filtered' ]]></command> <inputs> <param argument="--transcripts" name="assembly" type="data" format="fasta" label="Trinity assembly"/> <param argument="--matrix" type="data" format="tabular" label="Expression matrix"/> <param argument="--min_expr_any" type="float" optional="true" label="Minimum expression level required across any sample"/> <conditional name="isoform_filter"> <param name="isoform_mode" type="select" label="Isoform filtering method"> <option value="none">No filtering at the isoform level</option> <option value="highest_iso_only">Keep only the most highly expressed isoform per gene</option> <option value="min_pct_dom_iso">Keep all isoforms above a minimum percent of dominant expression</option> </param> <when value="none" /> <when value="highest_iso_only" /> <when value="min_pct_dom_iso"> <param argument="--min_pct_dom_iso" type="integer" value="" 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 value="no"> <param argument="--gene_to_trans_map" name="gene_trans_map" type="data" format="tabular" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" /> </when> </conditional> </section> </inputs> <outputs> <data format="fasta" 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"/> <param name="isoform_filter|isoform_mode" value="none"/> <output name="filtered" file="filtered/Trinity_filtered_exp.fasta" /> </test> <test> <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/> <param name="isoform_filter|isoform_mode" value="highest_iso_only"/> <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|isoform_mode" value="min_pct_dom_iso"/> <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: https://github.com/trinityrnaseq/trinityrnaseq/wiki </help> <expand macro="citation" /> </tool>