comparison analyze_diff_expr.xml @ 7:d61afd68a493 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4

6:c5f02e00d596

<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@.2">
    <description>from a Trinity assembly</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="2.6.0">bioconductor-qvalue</requirement>
        <requirement type="package" version="1.26.0">bioconductor-goseq</requirement>
        <requirement type="package" version="2.0.6">r-cluster</requirement>
    </expand>
    <command detect_errors="aggressive"><![CDATA[
    ## DE results input files must be in the working directory and have suffix .DE_results
    #import re
    #for $input in $DE_results
        #if re.search('.DE_results$',input.element_identifier)
            ## General case, where DE results files have been previously generated by run_de_analysis.pl
            ln -s "${input}" "${re.sub('[^\w\-_.]', '_', input.element_identifier)}"
        #else
            ## Particular case, where DE results files have non-standard names
            ln -s "${input}" "${re.sub('[^\w\-_.]', '_', input.element_identifier)}.DE_results"
        #end if
        &&
    #end for
    #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":
        ## DE matrix input files must be in the working directory and have the same name as DE results input files, but replacing suffix .DE_results by suffix .count_matrix
        #for $DE_matrix in $additional_params.GO_enrichment.DE_matrices
            ## Handle general case, where DE results files and DE matrix files have been previously generated by run_de_analysis.pl
            ln -s "${DE_matrix}" "${re.sub('[^\w\-_.]', '_', DE_matrix.element_identifier)}"
            &&
        #end for
    #end if

    analyze_diff_expr.pl
        --matrix "${matrix}"
        --samples "${samples}"
        -P ${p}
        -C ${c}

        #if str( $additional_params.max_DE_genes_per_comparison ):
            --max_DE_genes_per_comparison ${additional_params.max_DE_genes_per_comparison}

            --max_genes_clust ${additional_params.max_genes_clust}
        #end if

        #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":
            --examine_GO_enrichment
            --GO_annots "${$additional_params.GO_enrichment.GO_annots}"
            --gene_lengths "${$additional_params.GO_enrichment.gene_lengths}"
        #end if

        --output results
    ]]></command>
    <inputs>

        <test>
            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
            <param name="samples" value="count/samples.txt"/>
            <param name="DE_results">
                <collection type="list">
                    <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results" ftype="tabular" />
                    <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
                    <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
                </collection>
            </param>
            <section name="additional_params">
                <conditional name="GO_enrichment">
                    <param name="examine_GO_enrichment" value="yes"/>
                    <param name="DE_matrices">
                        <collection type="list">
                            <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix" value="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.count_matrix" ftype="tabular" />
                            <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix" value="count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
                            <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
                        </collection>
                    </param>
                    <param name="GO_annots" value="count/trinotate/go_annotations.txt"/>
                    <param name="gene_lengths" value="count/trinotate/genes.lengths.txt"/>

                <has_text text="--examine_GO_enrichment" />
                <has_text text="--GO_annots" />
                <has_text text="--gene_lengths" />
            </assert_command>
            <output_collection name="GOseq_enrichment">
                <element name="input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.wt_37-UP.subset.GOseq.enriched" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched"/>
            </output_collection>
        </test>
    </tests>
    <help>
<![CDATA[

7:d61afd68a493

<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@">
    <description>from a Trinity assembly</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="2.10.0">bioconductor-qvalue</requirement>
        <requirement type="package" version="1.30.0">bioconductor-goseq</requirement>
        <requirement type="package" version="2.0.6">r-cluster</requirement>
        <requirement type="package" version="1.1.24">r-fastcluster</requirement>
    </expand>
    <command detect_errors="aggressive"><![CDATA[
    ## DE results input files must be in the working directory and have suffix .DE_results
    #import re
    #for $input in $DE_results
        #if re.search('.DE_results$',input.element_identifier)
            ## General case, where DE results files have been previously generated by run_de_analysis.pl
            ln -s '${input}' "${re.sub('[^\w\-_.]', '_', input.element_identifier)}"
        #else
            ## Particular case, where DE results files have non-standard names
            ln -s '${input}' "${re.sub('[^\w\-_.]', '_', input.element_identifier)}.DE_results"
        #end if
        &&
    #end for
    #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":
        ## DE matrix input files must be in the working directory and have the same name as DE results input files, but replacing suffix .DE_results by suffix .count_matrix
        #for $DE_matrix in $additional_params.GO_enrichment.DE_matrices
            ## Handle general case, where DE results files and DE matrix files have been previously generated by run_de_analysis.pl
            ln -s '${DE_matrix}' "${re.sub('[^\w\-_.]', '_', DE_matrix.element_identifier)}"
            &&
        #end for
    #end if

    analyze_diff_expr.pl
        --matrix '${matrix}'
        --samples '${samples}'
        -P ${p}
        -C ${c}

        #if str( $additional_params.max_DE_genes_per_comparison ):
            --max_DE_genes_per_comparison ${additional_params.max_DE_genes_per_comparison}

            --max_genes_clust ${additional_params.max_genes_clust}
        #end if

        #if str( $additional_params.GO_enrichment.examine_GO_enrichment ) == "yes":
            --examine_GO_enrichment
            --GO_annots '${$additional_params.GO_enrichment.GO_annots}'
            --gene_lengths '${$additional_params.GO_enrichment.gene_lengths}'
        #end if

        --output results
    ]]></command>
    <inputs>

        <test>
            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
            <param name="samples" value="count/samples.txt"/>
            <param name="DE_results">
                <collection type="list">
                    <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results" ftype="tabular" />
                </collection>
            </param>
            <section name="additional_params">
                <conditional name="GO_enrichment">
                    <param name="examine_GO_enrichment" value="yes"/>
                    <param name="DE_matrices">
                        <collection type="list">
                            <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" value="count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.count_matrix" ftype="tabular" />
                        </collection>
                    </param>
                    <param name="GO_annots" value="count/trinotate/go_annotations.txt"/>
                    <param name="gene_lengths" value="count/trinotate/genes.lengths.txt"/>

                <has_text text="--examine_GO_enrichment" />
                <has_text text="--GO_annots" />
                <has_text text="--gene_lengths" />
            </assert_command>
            <output_collection name="GOseq_enrichment">
                <element name="input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.DE.subset.GOseq.enriched" compare="sim_size" file="count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.DE.subset.GOseq.enriched"/>
            </output_collection>
        </test>
    </tests>
    <help>
<![CDATA[