comparison align_and_estimate_abundance.xml @ 6:04bd98a9c751 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit bc4ea54f0deec4ddec8e6cf79fd547491e165686

5:be3607a306af

<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.0">
    <description>on a de novo assembly of RNA-Seq data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.3.0">rsem</requirement>
        <requirement type="package" version="1.5.1">express</requirement>
        <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 -->
        <requirement type="package" version="0.8.1">salmon</requirement>
    </expand>
    <command detect_errors="aggressive"><![CDATA[
        ln -f -s '$transcripts' input.fa &&

        #if $inputs.paired_or_single == "paired":

        <conditional name="method">
            <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
                <option value="RSEM">RSEM</option>
                <option value="eXpress">eXpress</option>
                <option value="salmon">Salmon</option>
            </param>
            <when value="RSEM">
                <param type="select" name="aln_method" argument="--aln_method" label="Alignment method">
                    <option value="bowtie">Bowtie</option>
                    <option value="bowtie2">Bowtie2</option>

            <when value="salmon">
                <param type="select" name="salmon_idx_type" argument="--salmon_idx_type" label="Index type">
                    <option value="quasi">Quasi</option>
                    <option value="fmd">FMD</option>
                </param>
            </when>
        </conditional>

        <section name="additional_params" title="Additional Options" expanded="False">
            <conditional name="gene_map">

            <filter>method['est_method'] == "salmon"</filter>
        </data>
        <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes">
            <filter>method['est_method'] == "salmon"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="paired_or_single" value="paired"/>
            <param name="left_input" value="reads.left.fq"/>

                    <has_line_matching expression="NA&#009;TRINITY_DN3_c0_g1.*" />
                    <has_n_columns n="15" />
                </assert_contents>
            </output>
        </test>
        <!-- test disabled because broken in travis, probably due to conda/symlink problem-->
        <!--test>
            <param name="paired_or_single" value="paired"/>
            <param name="left_input" value="reads.left.fq"/>
            <param name="right_input" value="reads.right.fq"/>
            <param name="transcripts" value="raw/Trinity.fasta"/>
            <param name="library_type" value="RF"/>

                <assert_contents>
                    <has_line_matching expression="TRINITY_DN3_c0_g1.*" />
                    <has_n_columns n="5" />
                </assert_contents>
            </output>
        </test-->
    </tests>
    <help>
<![CDATA[
Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
This tool estimates the abundance of isoforms and genes of a transcriptome assembled with Trinity, using FastQ of a specific sample.

6:04bd98a9c751

<tool id="trinity_align_and_estimate_abundance" name="Align reads and estimate abundance" version="@WRAPPER_VERSION@.2">
    <description>on a de novo assembly of RNA-Seq data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="1.3.0">rsem</requirement>
        <requirement type="package" version="1.5.1">express</requirement>
        <!-- Cannot update to salmon 0.8.2 because in Bioconda it requires icu 58, while r-base 3.3.1 requires icu 54 -->
        <requirement type="package" version="0.8.1">salmon</requirement>
        <requirement type="package" version="0.43.1">kallisto</requirement>
    </expand>
    <command detect_errors="aggressive"><![CDATA[
        ln -f -s '$transcripts' input.fa &&

        #if $inputs.paired_or_single == "paired":

        <conditional name="method">
            <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
                <option value="RSEM">RSEM</option>
                <option value="eXpress">eXpress</option>
                <option value="salmon">Salmon</option>
                <option value="kallisto">Kallisto</option>
            </param>
            <when value="RSEM">
                <param type="select" name="aln_method" argument="--aln_method" label="Alignment method">
                    <option value="bowtie">Bowtie</option>
                    <option value="bowtie2">Bowtie2</option>

            <when value="salmon">
                <param type="select" name="salmon_idx_type" argument="--salmon_idx_type" label="Index type">
                    <option value="quasi">Quasi</option>
                    <option value="fmd">FMD</option>
                </param>
            </when>
            <when value="kallisto">
            </when>
        </conditional>

        <section name="additional_params" title="Additional Options" expanded="False">
            <conditional name="gene_map">

            <filter>method['est_method'] == "salmon"</filter>
        </data>
        <data format="tabular" name="genes_counts_salmon" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/quant.sf.genes">
            <filter>method['est_method'] == "salmon"</filter>
        </data>

        <data format="tabular" name="isoforms_counts_kallisto" label="${tool.name} on ${on_string}: isoforms counts" from_work_dir="output/abundance.tsv">
            <filter>method['est_method'] == "kallisto"</filter>
        </data>
        <data format="tabular" name="genes_counts_kallisto" label="${tool.name} on ${on_string}: genes counts" from_work_dir="output/abundance.tsv.genes">
            <filter>method['est_method'] == "kallisto"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="paired_or_single" value="paired"/>
            <param name="left_input" value="reads.left.fq"/>

                    <has_line_matching expression="NA&#009;TRINITY_DN3_c0_g1.*" />
                    <has_n_columns n="15" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="paired_or_single" value="paired"/>
            <param name="left_input" value="reads.left.fq"/>
            <param name="right_input" value="reads.right.fq"/>
            <param name="transcripts" value="raw/Trinity.fasta"/>
            <param name="library_type" value="RF"/>

                <assert_contents>
                    <has_line_matching expression="TRINITY_DN3_c0_g1.*" />
                    <has_n_columns n="5" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="paired_or_single" value="paired"/>
            <param name="left_input" value="reads.left.fq"/>
            <param name="right_input" value="reads.right.fq"/>
            <param name="transcripts" value="raw/Trinity.fasta"/>
            <param name="library_type" value="RF"/>
            <param name="est_method" value="kallisto"/>
            <param name="has_gene_map" value="yes"/>
            <output name="isoforms_counts_kallisto">
                <assert_contents>
                    <has_line_matching expression="TRINITY_DN1_c0_g1_i1&#009;.*" />
                    <has_n_columns n="5" />
                </assert_contents>
            </output>
            <output name="genes_counts_kallisto">
                <assert_contents>
                    <has_line_matching expression="TRINITY_DN1_c0_g1&#009;.*" />
                    <has_n_columns n="5" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>
<![CDATA[
Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
This tool estimates the abundance of isoforms and genes of a transcriptome assembled with Trinity, using FastQ of a specific sample.