Mercurial > repos > recetox > recetox_aplcms_align_features

comparison recetox_aplcms_align_features.xml @ 1:148327f1e1be draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 699355cdf45b2157e9eea3962a01950d469fb0ba
author recetox
date Thu, 16 Jun 2022 10:23:01 +0000
parents e867e0c90d29
children 4d1583e15960
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0:e867e0c90d29 1:148327f1e1be
1 <tool id="recetox_aplcms_align_features" name="RECETOX apLCMS - align features" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="recetox_aplcms_align_features" name="RECETOX apLCMS - align features" version="@TOOL_VERSION@+galaxy1">
2 <description>align features from LC/MS spectra across samples</description> 2 <description>align features from LC/MS spectra across samples</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <import>macros_split.xml</import> 5 <import>macros_split.xml</import>
6 </macros> 6 </macros>
42 save_aligned_features(aligned, "$rt_cross_table", "$int_cross_table", "$tolerances") 42 save_aligned_features(aligned, "$rt_cross_table", "$int_cross_table", "$tolerances")
43 ]]></configfile> 43 ]]></configfile>
44 </configfiles> 44 </configfiles>
45 45
46 <inputs> 46 <inputs>
47 <param name="ms_files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="2" label="Input data" 47 <param name="ms_files" type="data_collection" collection_type="list" format="mzdata,mzml,mzxml,netcdf"
48 help="Mass spectrometry file for peak extraction." /> 48 label="Input data collection" help="Mass spectrometry file for peak extraction." />
49 <param name="corrected_files" type="data" format="parquet" multiple="true" min="2" 49 <param name="corrected_files" type="data_collection" collection_type="list" format="parquet"
50 label="Input corrected feature samples" 50 label="Input corrected feature samples collection"
51 help="Mass spectrometry files containing corrected feature samples." /> 51 help="Mass spectrometry files containing corrected feature samples." />
52 <expand macro="mz_tol_macro"/> 52 <expand macro="mz_tol_macro"/>
53 <param name="min_exp" type="integer" min="1" value="2" label="min_exp" 53 <param name="min_exp" type="integer" min="1" value="2" label="min_exp"
54 help="If a feature is to be included in the final feature table, it must be present in at least this number of spectra." /> 54 help="If a feature is to be included in the final feature table, it must be present in at least this number of spectra." />
55 <expand macro="peak_alignment"/> 55 <expand macro="peak_alignment"/>
61 <data name="int_cross_table" format="parquet" label="${tool.name} on ${on_string} (int cross table)" /> 61 <data name="int_cross_table" format="parquet" label="${tool.name} on ${on_string} (int cross table)" />
62 </outputs> 62 </outputs>
63 63
64 <tests> 64 <tests>
65 <test> 65 <test>
66 <param name="ms_files" value="mbr_test0.mzml,mbr_test1.mzml,mbr_test2.mzml" ftype="mzml"/> 66 <param name="ms_files">
67 <param name="corrected_files" ftype="parquet" 67 <collection type="list">
68 value="corrected_expected/corrected_0.parquet,corrected_expected/corrected_1.parquet,corrected_expected/corrected_2.parquet"/> 68 <element name="mbr_test0.mzml" value="mbr_test0.mzml"/>
69 <element name="mbr_test1.mzml" value="mbr_test1.mzml"/>
70 <element name="mbr_test2.mzml" value="mbr_test2.mzml"/>
71 </collection>
72 </param>
73 <param name="corrected_files">
74 <collection type="list">
75 <element name="corrected_features_0.parquet" value="corrected_expected/corrected_0.parquet"/>
76 <element name="corrected_features_1.parquet" value="corrected_expected/corrected_1.parquet"/>
77 <element name="corrected_features_2.parquet" value="corrected_expected/corrected_2.parquet"/>
78 </collection>
79 </param>
69 <output name="tolerances" file="tolerances.parquet" ftype="parquet"/> 80 <output name="tolerances" file="tolerances.parquet" ftype="parquet"/>
70 <output name="rt_cross_table" file="rt_cross_table.parquet" ftype="parquet"/> 81 <output name="rt_cross_table" file="rt_cross_table.parquet" ftype="parquet"/>
71 <output name="int_cross_table" file="int_cross_table.parquet" ftype="parquet"/> 82 <output name="int_cross_table" file="int_cross_table.parquet" ftype="parquet"/>
72 </test> 83 </test>
73 </tests> 84 </tests>