comparison filter_low_expr_transcripts.xml @ 19:aa38fa8c5815 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70

18:1fdb25a8384d

<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="bio_tools"/>

            > '$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>

                <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>

19:aa38fa8c5815

<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"/>

            > '$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>

                <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>