Mercurial > repos > recetox > recetox_aplcms_align_features
comparison recetox_aplcms_align_features.xml @ 1:148327f1e1be draft
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> |