annotate run_de_analysis.xml @ 3:83fa9ede1259 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit b9a2194247d728ef4d5a3c5511aa6ea63e9b2bcb

<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@.1">
    <description>using a Trinity assembly</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <!-- odering is crucial, otherwise R will override the ENV variables from deseq2 -->
        <requirement type="package" version="1.10.0">deseq2</requirement>
        <requirement type="package" version="3.14.0">bioconductor-edger</requirement>
        <requirement type="package" version="3.28.10">bioconductor-limma</requirement>
        <requirement type="package" version="1.10.0">bioconductor-deseq2</requirement>
    </expand>
    <expand macro="stdio"/>
    <command><![CDATA[

        ln -s "${matrix}" "input.matrix"

        &&

        run_DE_analysis.pl

        --matrix "input.matrix"

        --samples_file "${samples}"

        --method ${method_choice.method}

        #if $method_choice.method == "edgeR":
            --dispersion ${method_choice.edger_dispersion}
        #end if

        #if $method_choice.method == "ROTS":
            --ROTS_B ${method_choice.rots_b}
            --ROTS_K ${method_choice.rots_k}
        #end if

        --min_rowSum_counts ${additional_params.min_rowSum_counts}

        #if $additional_params.reference_sample:
            --reference_sample ${additional_params.reference_sample}
        #end if

        #if $additional_params.contrasts:
            --contrasts ${additional_params.contrasts}
        #end if

        --output results

    ]]></command>
    <inputs>
        <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
        <param format="tabular" name="samples" argument="--samples_file" type="data" label="Sample description" help="file describing samples and replicates"/>

        <conditional name="method_choice">
            <param type="select" name="method" argument="--method" label="Differential analysis method">
                <option value="edgeR">edgeR</option>
                <option value="DESeq2">DESeq2</option>
                <option value="voom">voom</option>
                <option value="ROTS">ROTS</option>
            </param>
            <when value="edgeR">
                <param name="edger_dispersion" argument="--dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" />
            </when>
            <when value="ROTS">
                <param name="rots_b" argument="--ROTS_B" type="integer" value="500" label="number of bootstraps and permutation resampling" />
                <param name="rots_k" argument="--ROTS_K" type="integer" value="5000" label="largest top genes size" />
            </when>
            <when value="voom">
            </when>
            <when value="DESeq2">
            </when>
        </conditional>

        <section name="additional_params" title="Additional Options" expanded="False">
            <param name="min_rowSum_counts" argument="--min_rowSum_counts" type="integer" value="2" label="Minimum count" help="Only those rows of matrix meeting requirement will be tested"/>
            <param name="reference_sample" argument="--reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/>
            <param format="tabular" name="contrasts" argument="--contrasts" optional="true" type="data" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/>
        </section>
    </inputs>
    <outputs>
        <collection name="DE_results" type="list" label="Differential expression results on ${on_string}">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.DE_results$" ext="tabular" directory="results" />
        </collection>
        <collection name="PDF_results" type="list" label="Differential expression plots on ${on_string}">
            <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf$" ext="pdf" directory="results" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
            <param name="samples" value="count/samples.txt"/>
            <param name="method" value="DESeq2"/>
            <output_collection name="DE_results">
                <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results"/>
                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results"/>
                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results"/>
            </output_collection>
            <output_collection name="PDF_results">
                <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf"/>
                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf"/>
            </output_collection>
        </test>
        <test>
            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
            <param name="samples" value="count/samples.txt"/>
            <param name="method" value="edgeR"/>
            <output_collection name="DE_results">
                <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results"/>
                <element name="input.matrix.wt_37_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results"/>
                <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results"/>
            </output_collection>
            <output_collection name="PDF_results">
                <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf"/>
                <element name="input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf"/>
                <element name="input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf"/>
            </output_collection>
        </test>
        <test>
            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
            <param name="samples" value="count/samples.txt"/>
            <param name="method" value="voom"/>
            <output_collection name="DE_results">
                <element name="input.matrix.wt_37_vs_wt_GSNO.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results"/>
                <element name="input.matrix.wt_37_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results"/>
                <element name="input.matrix.wt_GSNO_vs_wt_ph8.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results"/>
            </output_collection>
            <output_collection name="PDF_results">
                <element name="input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf"/>
                <element name="input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf"/>
                <element name="input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano" compare="sim_size" delta="100" file="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf"/>
            </output_collection>
        </test>
    </tests>
    <help>
<![CDATA[
Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
This tool performs differential expression analyses on a transcriptome assembled with Trinity.

**Inputs**

This tool uses the matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.

You must describe your samples and replicates with a tabular file looking like this:

=========== ================
ConditionA  CondA_replicate1
----------- ----------------
ConditionA  CondA_replicate2
----------- ----------------
ConditionB  CondB_replicate1
----------- ----------------
ConditionB  CondB_replicate2
----------- ----------------
ConditionC  CondC_replicate1
----------- ----------------
ConditionC  CondC_replicate2
----------- ----------------
ConditionC  CondC_replicate3
=========== ================


This file can be generated with the 'Describe samples and replicates' tool.
It will probably be the same file as used in the tool 'RNASeq samples quality check for transcript quantification'.
The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'.


.. _Trinity: http://trinityrnaseq.github.io
]]>
    </help>

    <expand macro="citation" />
</tool>