Mercurial > repos > recetox > matchms_split
view matchms_split.xml @ 8:5f1db71eceb2 draft
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 0f836e483fe3727580d6d1239135203b20812504
author | recetox |
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date | Wed, 22 Nov 2023 14:22:56 +0000 |
parents | ffe46a9b1124 |
children | 114617e6ad33 |
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<tool id="matchms_split" name="matchms split library" version="@TOOL_VERSION@+galaxy0" profile="21.09"> <description>split a large library into subsets</description> <macros> <import>macros.xml</import> <import>help.xml</import> </macros> <edam_operations> <edam_operation>operation_3359</edam_operation> </edam_operations> <expand macro="bio.tools"/> <expand macro="creator"/> <requirements> <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> </requirements> <command detect_errors='exit_code'><![CDATA[ python3 '$__tool_directory__/matchms_split.py' --filename '$msp_input' --method '${method.split_type}' --outdir 'output' #if $method.split_type == "chunk-size" --parameter ${method.chunk_size} #else if $method.split_type == "num-chunks" --parameter ${method.num_chunks} #end if ]]></command> <inputs> <param type="data" name="msp_input" format="msp" help="Spectral library (.msp) to split into smaller chunks. Requires keyword 'compound_name', 'compoundname' or 'name' to identify individual spectra using the one-per-file method."/> <conditional name="method"> <param name="split_type" type="select" label="Splitting method" display="radio" help="Method on how to split the library."> <option value="chunk-size" selected="true">Split into chunks of specified size</option> <option value="num-chunks">Split into specified number of chunks</option> <option value="one-per-file">Split to one spectrum per file</option> </param> <when value="chunk-size"> <param name="chunk_size" type="integer" value="1000" min="2" help="Number of spectra per output chunks."/> </when> <when value="num-chunks"> <param name="num_chunks" type="integer" value="5" min="2" help="Number of chunks into which to split the library."/> </when> <when value="one-per-file" /> </conditional> </inputs> <outputs> <collection format="msp" name="sample" type="list"> <discover_datasets pattern="__designation_and_ext__" ext="msp" directory="output"/> </collection > </outputs> <tests> <test> <param name="msp_input" value="split/sample_input.msp" /> <param name="split_type" value="one-per-file" /> <output_collection name="sample" type="list"> <element name="1NITROPYRENE" file="split/one-per-file/1NITROPYRENE.msp" ftype="msp" compare="diff"/> <element name="23DICHLOROPHENOL" file="split/one-per-file/23DICHLOROPHENOL.msp" ftype="msp" compare="diff"/> <element name="245TRICHLOROPHENOL" file="split/one-per-file/245TRICHLOROPHENOL.msp" ftype="msp" compare="diff"/> <element name="246TRICHLOROPHENOL" file="split/one-per-file/246TRICHLOROPHENOL.msp" ftype="msp" compare="diff"/> <element name="24DICHLOROPHENOL" file="split/one-per-file/24DICHLOROPHENOL.msp" ftype="msp" compare="diff"/> <element name="24DINITROPHENOL" file="split/one-per-file/24DINITROPHENOL.msp" ftype="msp" compare="diff"/> <element name="25DICHLOROPHENOL" file="split/one-per-file/25DICHLOROPHENOL.msp" ftype="msp" compare="diff"/> <element name="26DICHLOROPHENOL" file="split/one-per-file/26DICHLOROPHENOL.msp" ftype="msp" compare="diff"/> <element name="34DICHLOROPHENOL" file="split/one-per-file/34DICHLOROPHENOL.msp" ftype="msp" compare="diff"/> <element name="35DICHLOROPHENOL" file="split/one-per-file/35DICHLOROPHENOL.msp" ftype="msp" compare="diff"/> </output_collection> </test> <test> <param name="msp_input" value="split/sample_input.msp" /> <param name="split_type" value="num-chunks" /> <param name="num_chunks" value="2" /> <output_collection name="sample" type="list"> <element name="chunk_0" file="split/num-chunks/chunk_0.msp" ftype="msp" compare="diff"/> <element name="chunk_1" file="split/num-chunks/chunk_1.msp" ftype="msp" compare="diff"/> </output_collection> </test> <test> <param name="msp_input" value="split/sample_input.msp" /> <param name="split_type" value="chunk-size" /> <param name="chunk_size" value="4" /> <output_collection name="sample" type="list"> <element name="chunk_0" file="split/chunk-size/chunk_0.msp" ftype="msp" compare="diff"/> <element name="chunk_1" file="split/chunk-size/chunk_1.msp" ftype="msp" compare="diff"/> <element name="chunk_2" file="split/chunk-size/chunk_2.msp" ftype="msp" compare="diff"/> </output_collection> </test> </tests> <help> Description This tool can be used to split a mass spectral library into smaller subsets for further processing. This can be used to perform efficient spectral matching with large libraries, using job-level parallelism. Please observe that the `num-chunks` method does not preserve the order of the elements as it uses a `round robin` distribution. @HELP_matchms@ </help> <expand macro="citations"/> </tool>