Mercurial > repos > recetox > ramclustr

annotate ramclustr.xml @ 11:732777012256 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
author recetox
date Thu, 22 Jun 2023 11:44:43 +0000
parents 62bf6ef633d0
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
732777012256 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 10
diff changeset
1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy1" profile="21.09">
8
d9bcc43023c5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c321421a07bfdcc9ed423e9ed2ee794157984ba1
recetox
parents: 7
diff changeset
2 <description>A feature clustering algorithm for non-targeted mass spectrometric metabolomics data.</description>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
3 <macros>
3
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
4 <import>macros.xml</import>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
5 </macros>
11
732777012256 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 10
diff changeset
6 <edam_operations>
732777012256 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 10
diff changeset
7 <edam_operation>operation_3557</edam_operation>
732777012256 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 10
diff changeset
8 <edam_operation>operation_3435</edam_operation>
732777012256 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 10
diff changeset
9 <edam_operation>operation_3432</edam_operation>
732777012256 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 10
diff changeset
10 <edam_operation>operation_3465</edam_operation>
732777012256 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 10
diff changeset
11 </edam_operations>
732777012256 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 4a1bc7cba9745fd26e039b1629d4c9d9588ff5c0
recetox
parents: 10
diff changeset
12 <expand macro='annotation'/>
3
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
13 <expand macro="creator"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
14
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
15 <requirements>
1
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
16 <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>
10
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
17 <requirement type="package" version="3.20.0">bioconductor-xcms</requirement>
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
18 <requirement type="package" version="9.0.0">r-arrow</requirement>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
19 </requirements>
3
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
20
10
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
21 <command detect_errors="exit_code"><![CDATA[
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
22 Rscript
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
23 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
2
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
24 -e 'source("${ramclustr_method}")'
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
25 ]]>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
26 </command>
2
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
27 <configfiles>
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
28 <configfile name="ramclustr_method">
10
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
29 #if $filetype.type_choice == "xcms":
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
30 obj = load("$filetype.xcms.input_xcms")
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
31 ramclustObj = RAMClustR::rc.get.xcms.data(
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
32 xcmsObj = xdata,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
33 #if $extras.ExpDes:
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
34 ExpDes = load_experiment_definition("${$extras.ExpDes}"),
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
35 #end if
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
36 mzdec = $msp_output_details.mzdec,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
37 ensure.no.na = $extras.replace_zeros
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
38 )
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
39 #else if $filetype.type_choice == "csv":
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
40 ramclustObj = RAMClustR::rc.get.csv.data(
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
41 csv = "$filetype.ms_csv.ms",
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
42 #if $filetype.ms_csv.idmsms:
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
43 idmsms = "$filetype.ms_csv.idmsms",
2
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
44 #end if
10
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
45 #if $filetype.ms_csv.csv_phenoData:
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
46 phenoData = "$filetype.ms_csv.csv_phenoData",
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
47 #end if
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
48 #if $extras.ExpDes:
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
49 ExpDes = load_experiment_definition("${$extras.ExpDes}"),
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
50 #end if
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
51 st = $filetype.required.st,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
52 ensure.no.na = $extras.replace_zeros
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
53 )
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
54 #else if $filetype.type_choice == "recetox-aplcms":
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
55 ramclustObj = read_ramclustr_aplcms(
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
56 ms1_featuredefinitions = "$filetype.ms_dataframe.ms1_featureDefinitions",
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
57 ms1_featurevalues = "$filetype.ms_dataframe.ms1_featureValues",
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
58 #if $filetype.ms_dataframe.df_phenoData:
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
59 df_phenodata = "$filetype.ms_dataframe.df_phenoData",
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
60 phenodata_ext = "${filetype.ms_dataframe.df_phenoData.ext}",
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
61 #end if
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
62 #if $extras.ExpDes:
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
63 exp_des = "${$extras.ExpDes}",
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
64 #end if
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
65 st = $filetype.required.st,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
66 ensure_no_na = $extras.replace_zeros
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
67 )
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
68 #end if
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
69
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
70 #if $extras.replace_zeros == "TRUE":
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
71 ramclustObj = RAMClustR::rc.feature.replace.na(ramclustObj = ramclustObj)
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
72 #end if
10
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
73
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
74 #if $normalisation.normalisation_method.normalize != "none":
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
75 ramclustObj = apply_normalisation(
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
76 ramclustr_obj = ramclustObj,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
77 #if $normalisation.normalisation_method.normalize == "batch.qc":
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
78 metadata_file = "${$normalisation.normalisation_method.batch_order_qc}",
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
79 qc_inj_range = $normalisation.normalisation_method.qc_inj_range,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
80 #end if
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
81 #if $normalisation.normalisation_method.normalize == "qc":
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
82 metadata_file = "${$normalisation.normalisation_method.batch_order_qc}",
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
83 p_cut = $normalisation.normalisation_method.p_cut,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
84 rsq_cut = $normalisation.normalisation_method.rsq_cut,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
85 p_adjust = $normalisation.normalisation_method.p_adjust,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
86 #end if
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
87 normalize_method = "$normalisation.normalisation_method.normalize"
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
88 )
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
89 #end if
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
90
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
91 ramclustObj = RAMClustR::rc.ramclustr(
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
92 ramclustObj = ramclustObj,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
93 st = $filetype.required.st,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
94 sr = $filetype.required.sr,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
95 maxt = $filetype.required.maxt,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
96 deepSplit = $clustering.deepSplit,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
97 blocksize = $performance.blocksize,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
98 mult = $performance.mult,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
99 hmax = $clustering.hmax,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
100 minModuleSize = $clustering.minModuleSize,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
101 linkage = "$clustering.linkage",
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
102 cor.method = "$filetype.required.cor_method",
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
103 rt.only.low.n = $extras.rt_only_low_n,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
104 fftempdir = NULL,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
105 )
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
106
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
107 store_output(
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
108 ramclustr_obj = ramclustObj,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
109 output_merge_msp = $msp_output_details.merge_msp,
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
110 output_spec_abundance = "$spec_abundance",
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
111 #if $msp_output_details.merge_msp:
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
112 msp_file = "$mass_spectra_merged"
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
113 #else:
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
114 msp_file = NULL
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
115 #end if
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
116 )
2
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
117 </configfile>
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
118 </configfiles>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
119 <inputs>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
120 <conditional name="filetype">
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
121 <param name="type_choice" type="select" label="Choose input format:">
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
122 <option value="xcms" selected="true">XCMS</option>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
123 <option value="csv">CSV</option>
10
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
124 <option value="recetox-aplcms">RECETOX-APLCMS</option>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
125 </param>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
126 <when value="xcms">
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
127 <expand macro="parameters_xcms" />
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
128 <section name="required" title="General parameters" expanded="true">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
129 <param label="Sigma t" name="st" type="float" optional="true" help="Retention time similarity (optional).
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
130 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
131 <expand macro="parameters_required" />
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
132 </section>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
133 </when>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
134 <when value="csv">
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
135 <expand macro="parameters_csv" />
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
136 <section name="required" title="General parameters" expanded="true">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
137 <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity.
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
138 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
139 <expand macro="parameters_required" />
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
140 </section>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
141 </when>
10
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
142 <when value="recetox-aplcms">
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
143 <expand macro="parameters_recetox_aplcms" />
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
144 <section name="required" title="General parameters" expanded="true">
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
145 <param label="Sigma t" name="st" type="float" value="1" help="Retention time similarity.
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
146 A recommended starting point is half the value of your average chromatographic peak width at half max (seconds))."/>
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
147 <expand macro="parameters_required" />
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
148 </section>
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
149 </when>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
150 </conditional>
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
151 <expand macro="main_parameters" />
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
152 </inputs>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
153
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
154 <outputs>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
155 <data label="Spec Abundance of ${on_string}" name="spec_abundance" format="csv" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
156 <expand macro="output_msp"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
157 </outputs>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
158
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
159 <tests>
1
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
160 <test><!-- TEST 1 -->
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
161 <section name="filetype">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
162 <param name="type_choice" value="xcms"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
163 <section name="xcms">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
164 <param name="input_xcms" value="test1_xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
165 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
166 <section name="required">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
167 <param name="maxt" value="259.8"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
168 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
169 </section>
10
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
170 <section name="msp_output_details">
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
171 <param name="mzdec" value="4"/>
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
172 </section>
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
173 <section name="extras">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
174 <param name="ExpDes" value="lc-ramclustr-define-experiment.csv" ftype="csv"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
175 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
176 <output name="mass_spectra_merged" file="test1_fill_xcms_1.msp" ftype="msp"/>
1
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
177 <output name="spec_abundance" file="test1_spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
178 </test>
1
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
179 <test><!-- TEST 2 -->
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
180 <section name="filetype">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
181 <param name="type_choice" value="xcms"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
182 <section name="xcms">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
183 <param name="input_xcms" value="test2_xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
184 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
185 <section name="required">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
186 <param name="maxt" value="78.4"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
187 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
188 </section>
10
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
189 <section name="msp_output_details">
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
190 <param name="mzdec" value="4"/>
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
191 </section>
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
192 <section name="normalisation">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
193 <section name="normalisation_method">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
194 <param name="batch_order_qc" value="test2_sample_metadata_xcms_2.csv" ftype="csv" />
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
195 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
196 </section>
10
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
197 <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="sim_size" delta="100"/>
1
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
198 <output name="spec_abundance" file="test2_spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
199 </test>
1
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
200 <test><!-- TEST 3 -->
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
201 <section name="filetype">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
202 <param name="type_choice" value="csv"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
203 <section name="ms_csv">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
204 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
205 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
206 <section name="required">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
207 <param name="st" value="5.0"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
208 <param name="maxt" value="1"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
209 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
210 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
211 <section name="performance">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
212 <param name="blocksize" value="1000"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
213 <param name="mult" value="1"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
214 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
215 <output name="mass_spectra_merged" file="test3_spectra_csv_1.msp" ftype="msp"/>
1
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
216 <output name="spec_abundance" file="test3_spec_abundance_csv_1.csv" ftype="csv"/>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
217 </test>
1
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
218 <test><!-- TEST 4 -->
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
219 <section name="filetype">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
220 <param name="type_choice" value="csv"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
221 <section name="ms_csv">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
222 <param name="ms" value="test3_csv_test-input_1_2.csv" ftype="csv"/>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
223 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
224 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
225 <output name="mass_spectra_merged" file="test4_spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
226 </test>
10
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
227 <test><!-- TEST 5 -->
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
228 <section name="filetype">
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
229 <param name="type_choice" value="recetox-aplcms"/>
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
230 <section name="ms_dataframe">
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
231 <param name="ms1_featureDefinitions" value="test5_df_featureDefinitions_input.parquet" ftype="parquet"/>
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
232 <param name="ms1_featureValues" value="test5_df_featureValues_input.parquet" ftype="parquet"/>
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
233 </section>
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
234 </section>
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
235 <output name="mass_spectra_merged" file="test5_spectra.msp" ftype="msp" lines_diff="10"/>
62bf6ef633d0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 981ab05cdced6cbcbb1f13aa492e127365a4e9ed
recetox
parents: 9
diff changeset
236 </test>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
237 </tests>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
238
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
239 <help>
3
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
240 <![CDATA[
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
241 @HELP@
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
242
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
243 .. rubric:: **Footnotes**
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
244 .. [1] Correlation, Variance and Covariance - `stats::cor <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/cor>`_
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
245 .. [2] Hierarchical Clustering - `stats::hclust <https://www.rdocumentation.org/packages/stats/versions/3.6.2/topics/hclust>`_
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
246 .. [3] Dynamic Dendrogram Pruning Based on Dendrogram Only - `dynamicTreeCut::cutreeDynamicTree <https://www.rdocumentation.org/packages/dynamicTreeCut/versions/1.63-1/topics/cutreeDynamicTree>`_
3
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
247 ]]>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
248 </help>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
249
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
250 <expand macro="citations" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
251 </tool>