annotate filter_low_expr_transcripts.xml @ 13:42f93482524f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f3d9db3063d2cba26e6fbe82a3eee4e1a6fe0bd5"

<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>