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comparison matchms_split.xml @ 4:0cf68b536cd1 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
author recetox
date Tue, 27 Jun 2023 14:25:30 +0000
parents 169c72b2ce79
children 97be845e45c2
comparison
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3:9dfcee100f48 4:0cf68b536cd1
1 <tool id="matchms_split" name="matchms split library" version="@TOOL_VERSION@+galaxy0" python_template_version="3.7"> 1 <tool id="matchms_split" name="matchms split library" version="@TOOL_VERSION@+galaxy0" profile="21.09">
2 <description>split a large library into subsets</description>
2 <macros> 3 <macros>
3 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <import>help.xml</import>
4 </macros> 6 </macros>
5 7 <edam_operations>
8 <edam_operation>operation_3359</edam_operation>
9 </edam_operations>
10 <expand macro="bio.tools"/>
6 <expand macro="creator"/> 11 <expand macro="creator"/>
7 12
8 <requirements> 13 <requirements>
9 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> 14 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
10 </requirements> 15 </requirements>
46 <tests> 51 <tests>
47 <test> 52 <test>
48 <param name="msp_input" value="split/sample_input.msp" /> 53 <param name="msp_input" value="split/sample_input.msp" />
49 <param name="split_type" value="one-per-file" /> 54 <param name="split_type" value="one-per-file" />
50 <output_collection name="sample" type="list"> 55 <output_collection name="sample" type="list">
51 <element name="1NITROPYRENE" file="split/one-per-file/1NITROPYRENE.msp" ftype="msp" compare="contains"/> 56 <element name="1NITROPYRENE" file="split/one-per-file/1NITROPYRENE.msp" ftype="msp" compare="diff"/>
52 <element name="35DICHLOROPHENOL" file="split/one-per-file/35DICHLOROPHENOL.msp" ftype="msp" compare="contains"/> 57 <element name="23DICHLOROPHENOL" file="split/one-per-file/23DICHLOROPHENOL.msp" ftype="msp" compare="diff"/>
53 <element name="34DICHLOROPHENOL" file="split/one-per-file/34DICHLOROPHENOL.msp" ftype="msp" compare="contains"/> 58 <element name="245TRICHLOROPHENOL" file="split/one-per-file/245TRICHLOROPHENOL.msp" ftype="msp" compare="diff"/>
54 <element name="26DICHLOROPHENOL" file="split/one-per-file/26DICHLOROPHENOL.msp" ftype="msp" compare="contains"/> 59 <element name="246TRICHLOROPHENOL" file="split/one-per-file/246TRICHLOROPHENOL.msp" ftype="msp" compare="diff"/>
55 <element name="25DICHLOROPHENOL" file="split/one-per-file/25DICHLOROPHENOL.msp" ftype="msp" compare="contains"/> 60 <element name="24DICHLOROPHENOL" file="split/one-per-file/24DICHLOROPHENOL.msp" ftype="msp" compare="diff"/>
56 <element name="24DINITROPHENOL" file="split/one-per-file/24DINITROPHENOL.msp" ftype="msp" compare="contains"/> 61 <element name="24DINITROPHENOL" file="split/one-per-file/24DINITROPHENOL.msp" ftype="msp" compare="diff"/>
57 <element name="24DICHLOROPHENOL" file="split/one-per-file/24DICHLOROPHENOL.msp" ftype="msp" compare="contains"/> 62 <element name="25DICHLOROPHENOL" file="split/one-per-file/25DICHLOROPHENOL.msp" ftype="msp" compare="diff"/>
58 <element name="246TRICHLOROPHENOL" file="split/one-per-file/246TRICHLOROPHENOL.msp" ftype="msp" compare="contains"/> 63 <element name="26DICHLOROPHENOL" file="split/one-per-file/26DICHLOROPHENOL.msp" ftype="msp" compare="diff"/>
59 <element name="245TRICHLOROPHENOL" file="split/one-per-file/245TRICHLOROPHENOL.msp" ftype="msp" compare="contains"/> 64 <element name="34DICHLOROPHENOL" file="split/one-per-file/34DICHLOROPHENOL.msp" ftype="msp" compare="diff"/>
60 <element name="23DICHLOROPHENOL" file="split/one-per-file/23DICHLOROPHENOL.msp" ftype="msp" compare="contains"/> 65 <element name="35DICHLOROPHENOL" file="split/one-per-file/35DICHLOROPHENOL.msp" ftype="msp" compare="diff"/>
61 </output_collection> 66 </output_collection>
62 </test> 67 </test>
63 <test> 68 <test>
64 <param name="msp_input" value="split/sample_input.msp" /> 69 <param name="msp_input" value="split/sample_input.msp" />
65 <param name="split_type" value="num-chunks" /> 70 <param name="split_type" value="num-chunks" />
66 <param name="num_chunks" value="2" /> 71 <param name="num_chunks" value="2" />
67 <output_collection name="sample" type="list"> 72 <output_collection name="sample" type="list">
68 <element name="chunk_0" file="split/num-chunks/chunk_0.msp" ftype="msp" compare="contains"/> 73 <element name="chunk_0" file="split/num-chunks/chunk_0.msp" ftype="msp" compare="diff"/>
69 <element name="chunk_1" file="split/num-chunks/chunk_1.msp" ftype="msp" compare="contains"/> 74 <element name="chunk_1" file="split/num-chunks/chunk_1.msp" ftype="msp" compare="diff"/>
70 </output_collection> 75 </output_collection>
71 </test> 76 </test>
72 <test> 77 <test>
73 <param name="msp_input" value="split/sample_input.msp" /> 78 <param name="msp_input" value="split/sample_input.msp" />
74 <param name="split_type" value="chunk-size" /> 79 <param name="split_type" value="chunk-size" />
75 <param name="chunk_size" value="4" /> 80 <param name="chunk_size" value="4" />
76 <output_collection name="sample" type="list"> 81 <output_collection name="sample" type="list">
77 <element name="chunk_0" file="split/chunk-size/chunk_0.msp" ftype="msp" compare="contains"/> 82 <element name="chunk_0" file="split/chunk-size/chunk_0.msp" ftype="msp" compare="diff"/>
78 <element name="chunk_1" file="split/chunk-size/chunk_1.msp" ftype="msp" compare="contains"/> 83 <element name="chunk_1" file="split/chunk-size/chunk_1.msp" ftype="msp" compare="diff"/>
79 <element name="chunk_2" file="split/chunk-size/chunk_2.msp" ftype="msp" compare="contains"/> 84 <element name="chunk_2" file="split/chunk-size/chunk_2.msp" ftype="msp" compare="diff"/>
80 </output_collection> 85 </output_collection>
81 </test> 86 </test>
82 </tests> 87 </tests>
83 <help><![CDATA[ 88 <help>
84 Splitmsp handles input/output files in MSP format using the matchms.importing and matchms.exporting modules (https://matchms.readthedocs.io/en/latest/index.html). 89 Description
90 This tool can be used to split a mass spectral library into smaller subsets for further processing.
91 This can be used to perform efficient spectral matching with large libraries, using job-level parallelism.
85 92
86 Please observe that the `num-chunks` method does not preserve the order of the elements as it uses a `round robin` distribution. 93 Please observe that the `num-chunks` method does not preserve the order of the elements as it uses a `round robin` distribution.
87 ]]></help> 94
95 @HELP_matchms@
96 </help>
88 <expand macro="citations"/> 97 <expand macro="citations"/>
89 </tool> 98 </tool>