Mercurial > repos > recetox > recetox_aplcms_unsupervised

comparison recetox_aplcms_macros.xml @ 10:6057540f65a9 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox_aplcms commit 46f606d8d234807e603b55eb2791f76663b551ee"
author recetox
date Thu, 21 Oct 2021 15:03:18 +0000
parents 6925295ae5c3
children
comparison
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9:b18c2d014b28 10:6057540f65a9
3 <xml name="requirements"> 3 <xml name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="4.1.0">r-base</requirement> 5 <requirement type="package" version="4.1.0">r-base</requirement>
6 <requirement type="package" version="4.0.1">r-arrow</requirement> 6 <requirement type="package" version="4.0.1">r-arrow</requirement>
7 <requirement type="package" version="0.9.3">r-recetox-aplcms</requirement> 7 <requirement type="package" version="0.9.3">r-recetox-aplcms</requirement>
8 <requirement type="package" version="1.0.7">r-dplyr</requirement>
8 </requirements> 9 </requirements>
9 </xml> 10 </xml>
10 11
11 <xml name="creator"> 12 <xml name="creator">
12 <creator> 13 <creator>
17 <xml name="inputs"> 18 <xml name="inputs">
18 <inputs> 19 <inputs>
19 <param name="files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="3" label="data" 20 <param name="files" type="data" format="mzdata,mzml,mzxml,netcdf" multiple="true" min="3" label="data"
20 help="Mass spectrometry files for peak extraction." /> 21 help="Mass spectrometry files for peak extraction." />
21 <yield /> 22 <yield />
22 </inputs> 23 </inputs>
23 </xml> 24 </xml>
24 25
25 <xml name="history_db"> 26 <xml name="history_db">
26 <param name="known_table" type="data" format="parquet" label="known_table" 27 <param name="known_table" type="data" format="parquet" label="known_table"
27 help="A data table containing the known metabolite ions and previously found features. The table must contain these 18 columns: chemical_formula (optional), HMDB_ID (optional), KEGG_compound_ID (optional), neutral.mass (optional), ion.type (the ion form - optional), m.z (either theoretical or mean observed m/z value of previously found features), Number_profiles_processed (the total number of processed samples to build this database), Percent_found (the percentage of historically processed samples in which the feature appeared), mz_min (minimum observed m/z value), mz_max (maximum observed m/z value), RT_mean (mean observed retention time), RT_sd (standard deviation of observed retention time), RT_min (minimum observed retention time), RT_max (maximum observed retention time), int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity), int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." /> 28 help="A data table containing the known metabolite ions and previously found features. The table must contain these 18 columns: chemical_formula (optional), HMDB_ID (optional), KEGG_compound_ID (optional), neutral.mass (optional), ion.type (the ion form - optional), m.z (either theoretical or mean observed m/z value of previously found features), Number_profiles_processed (the total number of processed samples to build this database), Percent_found (the percentage of historically processed samples in which the feature appeared), mz_min (minimum observed m/z value), mz_max (maximum observed m/z value), RT_mean (mean observed retention time), RT_sd (standard deviation of observed retention time), RT_min (minimum observed retention time), RT_max (maximum observed retention time), int_mean.log. (mean observed log intensity), int_sd.log. (standard deviation of observed log intensity), int_min.log. (minimum observed log intensity), int_max.log. (maximum observed log intensity)." />
130 <param name="recover_min_count" type="integer" value="3" 131 <param name="recover_min_count" type="integer" value="3"
131 label="recover_min_count" 132 label="recover_min_count"
132 help="The minimum number of raw data points to be considered as a true feature." /> 133 help="The minimum number of raw data points to be considered as a true feature." />
133 </section> 134 </section>
134 </xml> 135 </xml>
136 <xml name="output_format">
137 <section name="output_format" title="Output Format">
138 <param name="out_format" type="boolean" checked="false" truevalue="recetox" falsevalue="original" label="Use custom RECETOX output format?" />
139 </section>
140 </xml>
135 141
136 <xml name="unsupervised_outputs"> 142 <xml name="unsupervised_outputs">
137 <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" /> 143 <data name="recovered_feature_sample_table" format="parquet" label="${tool.name} recovered_feature_sample_table on ${on_string}" />
138 <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" /> 144 <data name="aligned_feature_sample_table" format="parquet" label="${tool.name} aligned_feature_sample_table on ${on_string}" hidden="true" />
139 <collection name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}"> 145 <collection name="corrected_features" type="list" label="${tool.name} corrected_features on ${on_string}">