comparison ramclustr.xml @ 9:d70dd1d6ac4d draft

planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8775353ea1dddf10877441e158c7271a401d036e

8:c043e1fd79d1

<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy4" profile="21.09">
    <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='annotation'/>

            #if $extras.replace_zeros == "TRUE":
            ramclustObj = RAMClustR::rc.feature.replace.na(ramclustObj = ramclustObj)
            #end if

            #if $normalisation.normalisation_method.normalize != "none":
            ramclustObj = apply_normalisation(
                ramclustr_obj = ramclustObj,
                #if $normalisation.normalisation_method.normalize == "batch.qc":
                    metadata_file = "${$normalisation.normalisation_method.batch_order_qc}",

                    p_cut = $normalisation.normalisation_method.p_cut,
                    rsq_cut = $normalisation.normalisation_method.rsq_cut,
                    p_adjust = $normalisation.normalisation_method.p_adjust,
                #end if
                normalize_method = "$normalisation.normalisation_method.normalize"
            )
            #end if

            ramclustObj = RAMClustR::rc.ramclustr(
                ramclustObj = ramclustObj,

                linkage = "$clustering.linkage",
                cor.method = "$filetype.required.cor_method",
                rt.only.low.n = $extras.rt_only_low_n,
                fftempdir = NULL,
            )
            
            store_output(
                ramclustr_obj = ramclustObj,
                output_merge_msp = $msp_output_details.merge_msp,
                output_spec_abundance = "$spec_abundance",

                    <param name="ms1_featureValues" value="test5_df_featureValues_input.parquet" ftype="parquet"/>
                </section>
            </section>
            <output name="mass_spectra_merged" file="test5_spectra.msp" ftype="msp" lines_diff="10"/>
        </test>
    </tests>

    <help>
        <![CDATA[
            @HELP@

9:d70dd1d6ac4d

<tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy5" profile="21.09">
    <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='annotation'/>

            #if $extras.replace_zeros == "TRUE":
            ramclustObj = RAMClustR::rc.feature.replace.na(ramclustObj = ramclustObj)
            #end if

            #if $filtering.feature_filter_blanks.filter_blanks == "TRUE":
            ramclustObj = RAMClustR::rc.feature.filter.blanks(
                ramclustObj = ramclustObj,
                qc.tag = "${filtering.feature_filter_blanks.qc_tag}",
                blank.tag = "${filtering.feature_filter_blanks.blank_tag}",
                sn = $filtering.feature_filter_blanks.sn,
                remove.blanks = $filtering.feature_filter_blanks.remove_blanks
            )
            #end if

            #if $normalisation.normalisation_method.normalize != "none":
            ramclustObj = apply_normalisation(
                ramclustr_obj = ramclustObj,
                #if $normalisation.normalisation_method.normalize == "batch.qc":
                    metadata_file = "${$normalisation.normalisation_method.batch_order_qc}",

                    p_cut = $normalisation.normalisation_method.p_cut,
                    rsq_cut = $normalisation.normalisation_method.rsq_cut,
                    p_adjust = $normalisation.normalisation_method.p_adjust,
                #end if
                normalize_method = "$normalisation.normalisation_method.normalize"
            )
            #end if

            #if $filtering.feature_filter_cv.filter_cv == "TRUE":
            ramclustObj = RAMClustR::rc.feature.filter.cv(
                ramclustObj = ramclustObj,
                qc.tag = "${filtering.feature_filter_cv.qc_tag}",
                max.cv = $filtering.feature_filter_cv.max_cv
            )
            #end if

            ramclustObj = RAMClustR::rc.ramclustr(
                ramclustObj = ramclustObj,

                linkage = "$clustering.linkage",
                cor.method = "$filetype.required.cor_method",
                rt.only.low.n = $extras.rt_only_low_n,
                fftempdir = NULL,
            )

            #if $extras.quality_control == "TRUE":
            ramclustObj = RAMClustR::rc.qc(ramclustObj = ramclustObj)
            #end if
            
            store_output(
                ramclustr_obj = ramclustObj,
                output_merge_msp = $msp_output_details.merge_msp,
                output_spec_abundance = "$spec_abundance",

                    <param name="ms1_featureValues" value="test5_df_featureValues_input.parquet" ftype="parquet"/>
                </section>
            </section>
            <output name="mass_spectra_merged" file="test5_spectra.msp" ftype="msp" lines_diff="10"/>
        </test>
        <test expect_num_outputs="3"><!-- TEST 6 -->
            <section name="filetype">
                <param name="type_choice" value="xcms"/>
                <section name="xcms">
                    <param name="input_xcms" value="test6.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
                </section>
            </section>
            <section name="msp_output_details">
                <param name="mzdec" value="4"/>
            </section>
            <section name="extras">
                <param name="quality_control" value="TRUE"/>
            </section>
            <section name="filtering">
                <section name="feature_filter_blanks">
                    <param name="filter_blanks" value="TRUE"/>
                    <param name="blank_tag" value="Blanc"/>
                </section>
                <section name="feature_filter_cv">
                    <param name="filter_cv" value="TRUE"/>
                </section>
            </section>
            <output name="mass_spectra_merged" file="test6_out.msp" ftype="msp"/>
            <output name="spec_abundance">
                <assert_contents>
                    <has_size value="309" delta="10"/>
                </assert_contents>
            </output>
            <output name="pdf_plot">
                <assert_contents>
                    <has_size value="6842" delta="100"/>
                </assert_contents>
            </output>
        </test>
    </tests>

    <help>
        <![CDATA[
            @HELP@