view filter_low_expr_transcripts.xml @ 1:7246eeaad26d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 95f3e6a69bf939326c73a98e3306bccae8414ecd

<tool id="trinity_filter_low_expr_transcripts" name="Filter low expression transcripts" version="@WRAPPER_VERSION@.1">
    <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 $additional_params.gene_map.has_gene_map == "no":
                --gene_to_trans_map "$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_to_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>