Mercurial > repos > recetox > ramclustr_xcms
diff ramclustr_xcms.xml @ 3:405c8f8dc073 draft default tip
"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3479dea72f19e42832d30cda4283e56e81dd96d5"
| author | recetox |
|---|---|
| date | Mon, 07 Jun 2021 15:12:58 +0000 |
| parents | 8f4d04ad4acd |
| children |
line wrap: on
line diff
--- a/ramclustr_xcms.xml Thu Feb 04 11:34:30 2021 +0000 +++ b/ramclustr_xcms.xml Mon Jun 07 15:12:58 2021 +0000 @@ -1,4 +1,4 @@ -<tool id="ramclustr_xcms" name="RAMClustR (XCMS)" version="@TOOL_VERSION@+galaxy0"> +<tool id="ramclustr_xcms" name="RAMClustR (XCMS)" version="@TOOL_VERSION@+galaxy1"> <macros> <import>ramclustr_macros.xml</import> </macros> @@ -11,6 +11,7 @@ <param name="input_xcms" label="input_xcms" type="data" format="rdata.xcms.fillpeaks" help=": containing grouped feature data for clustering by ramclustR" /> <expand macro="parameters_required" /> <expand macro="parameters_optional_xcms" /> + <expand macro="parameters_optional_metadata" /> </inputs> <command detect_errors="aggressive"><![CDATA[ @@ -42,6 +43,9 @@ #if $optional.fftempdir fftempdir = $optional.fftempdir, #end if + #if $metadata.batch_order_qc + metadata_file = "${metadata.batch_order_qc}", + #end if )' -e 'store_output(x, "$result", "$method_metadata", $required.merge_msp, "$spec_abundance")' ]]> @@ -56,13 +60,23 @@ <tests> <test> - <param name="input_xcms" value="xcmsObj.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/> - <output name="result" file="ramclustObj.rdata" ftype="RData" compare="sim_size" delta="100"/> + <param name="input_xcms" value="xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/> + <output name="result" file="ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="100"/> <output_collection name="mass_spectra" type="list"> - <element name="fill" file="fill.msp" ftype="msp" checksum="md5$d53ed06d6f888a88ff321f833e29bb47"/> + <element name="fill" file="fill_xcms_1.msp" ftype="msp" checksum="md5$d53ed06d6f888a88ff321f833e29bb47"/> </output_collection> - <output name="method_metadata" file="metadata.txt" ftype="txt" checksum="md5$81db28b08860988e3966f585b0f44b0f"/> - <output name="spec_abundance" file="spec_abundance.csv" ftype="csv" compare="sim_size" delta="100"/> + <output name="method_metadata" file="metadata_xcms_1.txt" ftype="txt" checksum="md5$81db28b08860988e3966f585b0f44b0f"/> + <output name="spec_abundance" file="spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/> + </test> + <test> + <param name="input_xcms" value="xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/> + <param name="batch_order_qc" value="sample_metadata_xcms_2.csv" ftype="csv" /> + <output name="result" file="ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/> + <output_collection name="mass_spectra" type="list"> + <element name="fill" file="fill_xcms_2.msp" ftype="msp" lines_diff="10"/> + </output_collection> + <output name="method_metadata" file="metadata_xcms_2.txt" ftype="txt" checksum="md5$286e4aa53c38c99e92202584d7407406"/> + <output name="spec_abundance" file="spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/> </test> </tests>