Mercurial > repos > recetox > ramclustr

annotate ramclustr.xml @ 9:308bd645da47 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 8714723083359049eb1a715a946851e07f8a3a20
author recetox
date Tue, 20 Sep 2022 14:42:29 +0000
parents d9bcc43023c5
children 62bf6ef633d0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
308bd645da47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8714723083359049eb1a715a946851e07f8a3a20
recetox
parents: 8
diff changeset
1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy2">
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>
3
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
6 <expand macro="creator"/>
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
7
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
8 <requirements>
1
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
9 <requirement type="package" version="@TOOL_VERSION@">r-ramclustr</requirement>
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
10 <requirement type="package" version="3.14.0">bioconductor-xcms</requirement>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
11 </requirements>
3
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
12
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
13 <command detect_errors="aggressive"><![CDATA[
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
14 Rscript
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
15 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
2
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
16 -e 'source("${ramclustr_method}")'
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
17 ]]>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
18 </command>
2
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
19 <configfiles>
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
20 <configfile name="ramclustr_method">
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
21 store_output(
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
22 #if $filetype.type_choice == "xcms":
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
23 ramclustr_xcms(
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
24 input_xcms = "$filetype.xcms.input_xcms",
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
25 use_pheno = $filetype.xcms.usePheno,
2
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
26 #else:
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
27 ramclustr_csv(
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
28 ms = "$filetype.ms_csv.ms",
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
29 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
30 #end if
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
31 sr = $filetype.required.sr,
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
32 #if $filetype.type_choice == "xcms":
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
33 #if $filetype.required.st
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
34 st = $filetype.required.st,
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
35 #end if
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
36 #else:
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
37 st = $filetype.required.st,
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
38 #end if
2
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
39 cor_method = "$filetype.required.cor_method",
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
40 maxt = $filetype.required.maxt,
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
41 linkage = "$clustering.linkage",
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
42 min_module_size = $clustering.minModuleSize,
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
43 hmax = $clustering.hmax,
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
44 deep_split = "$clustering.deepSplit",
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
45 normalize = "$normalisation.normalisation_method.normalize",
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
46 #if "$normalisation.normalisation_method.normalize" == "batch.qc":
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
47 metadata_file = "$normalisation.normalisation_method.batch_order_qc",
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
48 qc_inj_range = $normalisation.normalisation_method.qc_inj_range,
2
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
49 #end if
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
50 block_size = $performance.blocksize,
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
51 mult = $performance.mult,
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
52 mzdec = $msp_output_details.mzdec,
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
53 rt_only_low_n = $extras.rt_only_low_n,
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
54 replace_zeros = $extras.replace_zeros,
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
55 #if $extras.ExpDes:
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
56 exp_design = "${$extras.ExpDes}"
4
69e0da4703b5 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit b514d9bf91b62bb06d39e6ceee21d8f18876e12b"
recetox
parents: 3
diff changeset
57 #end if
2
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
58 ),
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
59 $msp_output_details.merge_msp,
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
60 "$spec_abundance",
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
61 #if $msp_output_details.merge_msp:
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
62 "$mass_spectra_merged"
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
63 #else:
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
64 NULL
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
65 #end if
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
66 )
2
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
67 </configfile>
eac0e6feb850 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit d4a601c637b18f18a5cda9111208559e72d12657"
recetox
parents: 1
diff changeset
68 </configfiles>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
69 <inputs>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
70 <conditional name="filetype">
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
71 <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
72 <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
73 <option value="csv">CSV</option>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
74 </param>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
75 <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
76 <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
77 <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
78 <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
79 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
80 <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
81 </section>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
82 </when>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
83 <when value="csv">
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
84 <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
85 <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
86 <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
87 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
88 <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
89 </section>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
90 </when>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
91 </conditional>
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
92 <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
93 </inputs>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
94
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
95 <outputs>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
96 <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
97 <expand macro="output_msp"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
98 </outputs>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
99
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
100 <tests>
1
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
101 <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
102 <section name="filetype">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
103 <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
104 <section name="xcms">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
105 <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
106 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
107 <section name="required">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
108 <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
109 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
110 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
111 <section name="extras">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
112 <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
113 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
114 <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
115 <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
116 </test>
1
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
117 <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
118 <section name="filetype">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
119 <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
120 <section name="xcms">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
121 <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
122 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
123 <section name="required">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
124 <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
125 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
126 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
127 <section name="normalisation">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
128 <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
129 <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
130 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
131 </section>
9
308bd645da47 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 8714723083359049eb1a715a946851e07f8a3a20
recetox
parents: 8
diff changeset
132 <output name="mass_spectra_merged" file="test2_fill_xcms_2.msp" ftype="msp" compare="diff" lines_diff="20"/>
1
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
133 <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
134 </test>
1
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
135 <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
136 <section name="filetype">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
137 <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
138 <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
139 <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
140 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
141 <section name="required">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
142 <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
143 <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
144 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
145 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
146 <section name="performance">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
147 <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
148 <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
149 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
150 <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
151 <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
152 </test>
1
15e173c5762c "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 249fdcc40e08fb1aece6d119fcf747eea1c595fb"
recetox
parents: 0
diff changeset
153 <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
154 <section name="filetype">
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
155 <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
156 <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
157 <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
158 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
159 </section>
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
160 <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
161 </test>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
162 </tests>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
163
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
164 <help>
3
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
165 <![CDATA[
211cd88b5148 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
recetox
parents: 2
diff changeset
166 @HELP@
5
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
167
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
168 .. rubric:: **Footnotes**
10ded21d47c0 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit 3d2821ffc97cc4f9287ee83bbddb306a8034daa0"
recetox
parents: 4
diff changeset
169 .. [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
170 .. [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
171 .. [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
172 ]]>
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
173 </help>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
174
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
175 <expand macro="citations" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
176 </tool>