Mercurial > repos > recetox > ramclustr
diff ramclustr.xml @ 5:10ded21d47c0 draft
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
| author | recetox |
|---|---|
| date | Fri, 11 Feb 2022 14:14:38 +0000 |
| parents | 69e0da4703b5 |
| children | 8d6f7543a56a |
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--- a/ramclustr.xml Fri Feb 04 08:31:26 2022 +0000 +++ b/ramclustr.xml Fri Feb 11 14:14:38 2022 +0000 @@ -20,51 +20,49 @@ store_output( #if $filetype.type_choice == "xcms": ramclustr_xcms( - input_xcms = "$filetype.input_xcms", + input_xcms = "$filetype.xcms.input_xcms", + use_pheno = $filetype.xcms.usePheno, #else: ramclustr_csv( - ms="$filetype.ms_csv.ms", - idmsms="$filetype.ms_csv.idmsms", - feature_delimiter="$filetype.ms_csv.feature_delimiter", - sample_name_column = $filetype.ms_csv.sample_name_column, - retention_time_column= $filetype.ms_csv.retention_time_column, + ms = "$filetype.ms_csv.ms", + idmsms = "$filetype.ms_csv.idmsms", #end if sr = $filetype.required.sr, - deep_split = $filetype.required.deepSplit, - block_size = $filetype.required.blocksize, - mult = $filetype.required.mult, - hmax = $filetype.required.hmax, - collapse = $filetype.required.collapse, - use_pheno = $filetype.required.usePheno, - qc_inj_range = $filetype.required.qc_inj_range, - normalize = "$filetype.required.normalize", - min_module_size = $filetype.required.minModuleSize, - linkage = "$filetype.required.linkage", - mzdec = $filetype.required.mzdec, + #if $filetype.type_choice == "xcms": + #if $filetype.required.st + st = $filetype.required.st, + #end if + #else: + st = $filetype.required.st, + #end if cor_method = "$filetype.required.cor_method", - rt_only_low_n = $filetype.required.rt_only_low_n, - replace_zeros = $filetype.required.replace_zeros, - #if $filetype.type_choice == "xcms": - #if $filetype.optional.st - st = $filetype.optional.st, + maxt = $filetype.required.maxt, + linkage = "$clustering.linkage", + min_module_size = $clustering.minModuleSize, + hmax = $clustering.hmax, + deep_split = "$clustering.deepSplit", + normalize = "$normalisation.normalisation_method.normalize", + #if "$normalisation.normalisation_method.normalize" == "batch.qc": + metadata_file = "$normalisation.normalisation_method.batch_order_qc", + qc_inj_range = $normalisation.normalisation_method.qc_inj_range, #end if - #else: - st = $filetype.ms_csv.st, - #end if - #if $filetype.optional.maxt - maxt = $filetype.optional.maxt, - #end if - #if $filetype.optional.fftempdir - fftempdir = $filetype.optional.fftempdir, - #end if - #if $filetype.metadata.batch_order_qc - metadata_file = "${filetype.metadata.batch_order_qc}", - #end if - #if $filetype.metadata.ExpDes - exp_design = "${filetype.metadata.ExpDes}" + block_size = $performance.blocksize, + mult = $performance.mult, + mzdec = $msp_output_details.mzdec, + rt_only_low_n = $extras.rt_only_low_n, + replace_zeros = $extras.replace_zeros, + #if $extras.ExpDes: + exp_design = "${$extras.ExpDes}" #end if ), - "$result", "$method_metadata", $filetype.required.merge_msp, "$spec_abundance") + $msp_output_details.merge_msp, + "$spec_abundance", + #if $msp_output_details.merge_msp: + "$mass_spectra_merged" + #else: + NULL + #end if + ) </configfile> </configfiles> <inputs> @@ -74,80 +72,102 @@ <option value="csv">CSV</option> </param> <when value="xcms"> - <param name="input_xcms" label="input_xcms" type="data" format="rdata.xcms.fillpeaks" help="Grouped feature data for clustering by ramclustR" /> - <expand macro="parameters_required" /> - <expand macro="parameters_optional_xcms" /> - <expand macro="parameters_optional_metadata" /> + <expand macro="parameters_xcms" /> + <section name="required" title="General parameters" expanded="true"> + <param label="Sigma t" name="st" type="float" optional="true" help="Retention time similarity (optional). + A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/> + <expand macro="parameters_required" /> + </section> </when> <when value="csv"> <expand macro="parameters_csv" /> - <expand macro="parameters_required" /> - <expand macro="parameters_optional_csv" /> - <expand macro="parameters_optional_metadata" /> + <section name="required" title="General parameters" expanded="true"> + <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity. + A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/> + <expand macro="parameters_required" /> + </section> </when> </conditional> + <expand macro="main_parameters" /> </inputs> <outputs> - <data label="${tool.name} on ${on_string}" name="result" format="RData" /> <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" /> - <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/> <expand macro="output_msp"/> </outputs> <tests> <test><!-- TEST 1 --> - <param name="type_choice" value="xcms"/> - <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/> - <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/> - <output name="result" file="test1_ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="200"/> - <output_collection name="mass_spectra" type="list"> - <element name="experiment_lc" file="test1_fill_xcms_1.msp" ftype="msp"/> - </output_collection> - <output name="method_metadata" file="test1_metadata_xcms_1.txt" ftype="txt"/> + <section name="filetype"> + <param name="type_choice" value="xcms"/> + <section name="xcms"> + <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/> + </section> + <section name="required"> + <param name="maxt" value="259.8"/> + </section> + </section> + <section name="extras"> + <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/> + </section> + <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/> <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/> </test> <test><!-- TEST 2 --> - <param name="type_choice" value="xcms"/> - <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/> - <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" /> - <output name="result" file="test2_ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/> - <output_collection name="mass_spectra" type="list"> - <element name="fill" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="10"/> - </output_collection> - <output name="method_metadata" file="test2_metadata_xcms_2.txt" ftype="txt"/> + <section name="filetype"> + <param name="type_choice" value="xcms"/> + <section name="xcms"> + <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/> + </section> + <section name="required"> + <param name="maxt" value="78.4"/> + </section> + </section> + <section name="normalisation"> + <section name="normalisation_method"> + <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" /> + </section> + </section> + <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="10"/> <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/> </test> <test><!-- TEST 3 --> - <param name="type_choice" value="csv"/> - <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/> - <param name="st" value="5.0"/> - <param name="blocksize" value="1000"/> - <param name="mult" value="1"/> - <param name="maxt" value="1"/> - <output name="result" file="test3_ramclustObj_csv_1.rdata" ftype="RData" compare="sim_size" delta="200"/> + <section name="filetype"> + <param name="type_choice" value="csv"/> + <section name="ms_csv"> + <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/> + </section> + <section name="required"> + <param name="st" value="5.0"/> + <param name="maxt" value="1"/> + </section> + </section> + <section name="performance"> + <param name="blocksize" value="1000"/> + <param name="mult" value="1"/> + </section> + <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/> <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/> - <output name="method_metadata" file="test3_metadata_csv_1.txt" ftype="txt"/> - <output_collection name="mass_spectra" type="list"> - <element name="fill" file="test3_spectra_csv_1.msp" ftype="msp"/> - </output_collection> </test> <test><!-- TEST 4 --> - <param name="type_choice" value="csv"/> - <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/> - <param name="batch_order_qc" value="test4_sample_metadata_csv_2.csv" ftype="csv" /> - <output name="result" file="test4_ramclustObj_csv_2.rdata" ftype="RData" compare="sim_size" delta="200"/> - <output name="spec_abundance" file="test4_spec_abundance_csv_2.csv" ftype="csv"/> - <output name="method_metadata" file="test4_metadata_csv_2.txt" ftype="txt"/> - <output_collection name="mass_spectra" type="list"> - <element name="fill" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/> - </output_collection> + <section name="filetype"> + <param name="type_choice" value="csv"/> + <section name="ms_csv"> + <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/> + </section> + </section> + <output name="mass_spectra_merged" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/> </test> </tests> <help> <![CDATA[ @HELP@ + + .. rubric:: **Footnotes** + .. [1] Correlation, Variance and Covariance - `stats::cor <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/cor>`_ + .. [2] Hierarchical Clustering - `stats::hclust <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/hclust>`_ + .. [3] Dynamic Dendrogram Pruning Based on Dendrogram Only - `dynamicTreeCut::cutreeDynamicTree <https://www.rdocumentation.org/packages/dynamicTreeCut/versions/1.63-1/topics/cutreeDynamicTree>`_ ]]> </help>