diff --git a/tools/aplcms/.shed.yml b/tools/aplcms/.shed.yml
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+owner: recetox
+remote_repository_url: "https://github.com/RECETOX/galaxytools/tree/master/tools/aplcms"
+homepage_url: "http://web1.sph.emory.edu/apLCMS/"
+categories:
+ - Metabolomics
+repositories:
+ recetox_aplcms_unsupervised:
+ description: "Generate a feature table from a batch of LC/MS spectra using apLCMS's Unsupervised method."
+ include:
+ - aplcms_unsupervised.xml
+ - aplcms_macros.xml
+ recetox_aplcms_hybrid:
+ description: "Generate a feature table from a batch of LC/MS spectra using apLCMS's Hybrid method."
+ include:
+ - aplcms_hybrid.xml
+ - aplcms_macros.xml
diff --git a/tools/aplcms/aplcms_hybrid.xml b/tools/aplcms/aplcms_hybrid.xml
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+ aplcms_macros.xml
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+ This is the Hybrid version of apLCMS which is incorporating the knowledge of known metabolites and historically
+ detected features on the same machinery to help detect and quantify lower-intensity peaks.
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+ CAUTION: To use such knowledge, especially historical data, you must keep using (1) the same chromatography
+ system (otherwise the retention time will not match), and (2) the same type of samples with similar extraction
+ technique, such as human serum.
+
+ @GENERAL_HELP@
+
+
+
+
diff --git a/tools/aplcms/aplcms_macros.xml b/tools/aplcms/aplcms_macros.xml
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+ 6.6.6
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+ recetox_datatypes
+ recetox/aplcms:6.6.6-recetox0
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+ apLCMS is a software which generates a feature table from a batch of LC/MS spectra. The m/z and retention time
+ tolerance levels are estimated from the data. A run-filter is used to detect peaks and remove noise.
+ Non-parametric statistical methods are used to find-tune peak selection and grouping. After retention time
+ correction, a feature table is generated by aligning peaks across spectra. For further information on apLCMS
+ please refer to http://web1.sph.emory.edu/apLCMS.
+
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+ 10.1093/bioinformatics/btp291
+ 10.1186/1471-2105-11-559
+ 10.1021/pr301053d
+ 10.1093/bioinformatics/btu430
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diff --git a/tools/aplcms/aplcms_unsupervised.xml b/tools/aplcms/aplcms_unsupervised.xml
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+ aplcms_macros.xml
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+ This is the Unsupervised version of apLCMS which is not relying on any existing knowledge about metabolites or
+ any historically detected features. For such functionality please use the Hybrid version of apLCMS.
+
+ @GENERAL_HELP@
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