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filter_low_expr_transcripts.xml
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filter_low_expr_transcripts.xml
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<tool id="trinity_filter_low_expr_transcripts" name="Filter low expression transcripts" version="@WRAPPER_VERSION@">
<description>from a Trinity assembly</description>
<macros>
<import>macros.xml</import>
</macros>
<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 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="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: http://trinityrnaseq.github.io
</help>
<expand macro="citation" />
</tool>