Mercurial > repos > recetox > ramclustr

annotate ramclustr.xml @ 0:cb0b83b330fd 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 c69f8d9772bdb9fb3cc9473651397cd6bb877020"
author recetox
date Wed, 28 Jul 2021 08:42:02 +0000
parents
children 15e173c5762c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
1 <tool id="ramclustr" name="RAMClustR" version="@TOOL_VERSION@+galaxy1">
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
2 <macros>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
3 <import>ramclustr_macros.xml</import>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
4 </macros>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
5
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
6 <requirements>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
7 <container type="docker">recetox/ramclustr:1.1.0-recetox0</container>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
8 </requirements>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
9
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
10 <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
11 Rscript
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
12 -e 'source("${__tool_directory__}/ramclustr_wrapper.R")'
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
13 #if $filetype.type_choice == "xcms":
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
14 -e 'x <- ramclustr_xcms(
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
15 input_xcms = "$filetype.input_xcms",
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
16 #else:
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
17 -e 'x <- ramclustr_csv(
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
18 ms="$filetype.ms_csv.ms",
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
19 idmsms="$filetype.ms_csv.idmsms",
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
20 feature_delimiter="$filetype.ms_csv.feature_delimiter",
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
21 sample_name_column = $filetype.ms_csv.sample_name_column,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
22 retention_time_column= $filetype.ms_csv.retention_time_column,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
23 #end if
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
24 sr = $filetype.required.sr,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
25 deep_split = $filetype.required.deepSplit,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
26 block_size = $filetype.required.blocksize,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
27 mult = $filetype.required.mult,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
28 hmax = $filetype.required.hmax,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
29 collapse = $filetype.required.collapse,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
30 use_pheno = $filetype.required.usePheno,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
31 qc_inj_range = $filetype.required.qc_inj_range,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
32 normalize = "$filetype.required.normalize",
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
33 min_module_size = $filetype.required.minModuleSize,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
34 linkage = "$filetype.required.linkage",
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
35 mzdec = $filetype.required.mzdec,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
36 cor_method = "$filetype.required.cor_method",
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
37 rt_only_low_n = $filetype.required.rt_only_low_n,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
38 replace_zeros = $filetype.required.replace_zeros,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
39 #if $filetype.type_choice == "xcms":
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
40 #if $filetype.optional.st
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
41 st = $filetype.optional.st,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
42 #end if
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
43 #else:
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
44 st = $filetype.ms_csv.st,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
45 #end if
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
46 #if $filetype.optional.maxt
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
47 maxt = $filetype.optional.maxt,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
48 #end if
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
49 #if $filetype.optional.fftempdir
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
50 fftempdir = $filetype.optional.fftempdir,
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
51 #end if
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
52 #if $filetype.metadata.batch_order_qc
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
53 metadata_file = "${filetype.metadata.batch_order_qc}",
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
54 #end if
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
55 )'
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
56 -e 'store_output(x, "$result", "$method_metadata", $filetype.required.merge_msp, "$spec_abundance")'
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
57 ]]>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
58 </command>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
59
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
60 <inputs>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
61 <conditional name="filetype">
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
62 <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
63 <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
64 <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
65 </param>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
66 <when value="xcms">
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
67 <param name="input_xcms" label="input_xcms" type="data" format="rdata.xcms.fillpeaks" help=": containing grouped feature data for clustering by ramclustR" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
68 <expand macro="parameters_required" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
69 <expand macro="parameters_optional_xcms" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
70 <expand macro="parameters_optional_metadata" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
71 </when>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
72 <when value="csv">
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
73 <expand macro="parameters_csv" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
74 <expand macro="parameters_required" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
75 <expand macro="parameters_optional_csv" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
76 <expand macro="parameters_optional_metadata" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
77 </when>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
78 </conditional>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
79 </inputs>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
80
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
81 <outputs>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
82 <data label="${tool.name} on ${on_string}" name="result" format="RData" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
83 <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
84 <data label="Metadata for ${tool.name} on ${on_string}" name="method_metadata" format="txt"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
85 <expand macro="output_msp"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
86 </outputs>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
87
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
88 <tests>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
89 <test>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
90 <param name="type_choice" value="xcms"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
91 <param name="input_xcms" value="xcmsObj_1.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
92 <output name="result" file="ramclustObj_xcms_1.rdata" ftype="RData" compare="sim_size" delta="100"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
93 <output_collection name="mass_spectra" type="list">
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
94 <element name="fill" file="fill_xcms_1.msp" ftype="msp" checksum="md5$d53ed06d6f888a88ff321f833e29bb47"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
95 </output_collection>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
96 <output name="method_metadata" file="metadata_xcms_1.txt" ftype="txt" checksum="md5$81db28b08860988e3966f585b0f44b0f"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
97 <output name="spec_abundance" file="spec_abundance_xcms_1.csv" ftype="csv" compare="sim_size" delta="100"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
98 </test>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
99 <test>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
100 <param name="type_choice" value="xcms"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
101 <param name="input_xcms" value="xcmsObj_2.rdata.xcms.fillpeaks" ftype="rdata.xcms.fillpeaks"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
102 <param name="batch_order_qc" value="sample_metadata_xcms_2.csv" ftype="csv" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
103 <output name="result" file="ramclustObj_xcms_2.rdata" ftype="RData" compare="sim_size" delta="200"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
104 <output_collection name="mass_spectra" type="list">
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
105 <element name="fill" file="fill_xcms_2.msp" ftype="msp" lines_diff="10"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
106 </output_collection>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
107 <output name="method_metadata" file="metadata_xcms_2.txt" ftype="txt" checksum="md5$286e4aa53c38c99e92202584d7407406"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
108 <output name="spec_abundance" file="spec_abundance_xcms_2.csv" ftype="csv" compare="sim_size" delta="100"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
109 </test>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
110 <test>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
111 <param name="type_choice" value="csv"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
112 <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
113 <param name="sample_name_column" value="1"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
114 <param name="feature_delimiter" value="_"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
115 <param name="retention_time_column" value="2"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
116 <param name="st" value="5.0"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
117 <param name="sr" value="0.5"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
118 <param name="deepSplit" value="False"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
119 <param name="blocksize" value="1000"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
120 <param name="mult" value="1"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
121 <param name="hmax" value="0.3"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
122 <param name="collapse" value="True"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
123 <param name="usePheno" value="True"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
124 <param name="normalize" value="none"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
125 <param name="qc_inj_range" value="20"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
126 <param name="minModuleSize" value="2"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
127 <param name="linkage" value="average"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
128 <param name="mzdec" value="3"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
129 <param name="cor_method" value="pearson"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
130 <param name="rt_only_low_n" value="True"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
131 <param name="replace_zeros" value="True"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
132 <param name="Merge MSP Files" value="True"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
133 <param name="maxt" value="1"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
134 <output name="result" file="ramclustObj_csv_1.rdata"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
135 <output name="spec_abundance" file="spec_abundance_csv_1.csv" ftype="csv"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
136 <output name="method_metadata" file="metadata_csv_1.txt" ftype="txt"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
137 <output_collection name="mass_spectra" type="list">
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
138 <element name="fill" file="spectra_csv_1.msp" ftype="msp"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
139 </output_collection>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
140 </test>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
141 <test>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
142 <param name="type_choice" value="csv"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
143 <param name="ms" value="csv_test-input_1_2.csv" ftype="csv"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
144 <param name="sample_name_column" value="1"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
145 <param name="feature_delimiter" value="_"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
146 <param name="retention_time_column" value="2"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
147 <param name="batch_order_qc" value="sample_metadata_csv_2.csv" ftype="csv" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
148 <output name="result" file="ramclustObj_csv_2.rdata"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
149 <output name="spec_abundance" file="spec_abundance_csv_2.csv" ftype="csv"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
150 <output name="method_metadata" file="metadata_csv_2.txt" ftype="txt"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
151 <output_collection name="mass_spectra" type="list">
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
152 <element name="fill" file="spectra_csv_2.msp" ftype="msp" lines_diff="10"/>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
153 </output_collection>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
154 </test>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
155 </tests>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
156
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
157 <help>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
158 Documentation
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
159 For documentation on the tool see https://github.com/cbroeckl/RAMClustR/blob/master/vignettes/RAMClustR.Rmd
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
160
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
161 Upstream Tools
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
162 +-------+----------------------+----------------------+------------+
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
163 | Name | Output File | Format | Parameter |
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
164 +=======+======================+======================+============+
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
165 | xcms | xset.fillPeaks.RData | rdata.xcms.fillpeaks | xcmsObj |
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
166 +-------+----------------------+----------------------+------------+
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
167
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
168 The tool takes an **xcmsSet** object as input and extracts all relevant information.
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
169
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
170 +-------+------------------------+--------+------------+
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
171 | Name | Output File | Format | Parameter |
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
172 +=======+========================+========+============+
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
173 | ??? | Feature Table with MS1 | csv | ms |
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 | ??? | Feature Table with MS2 | csv | idmsms |
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
176 +-------+------------------------+--------+------------+
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
177
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
178 Alternatively, the tool takes a **csv** table as input which has to fulfill the following requirements
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
179
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
180 (1) no more than one sample (or file) name column and one feature name row;
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
181 (2) feature names that contain the mass and retention times, separated by a constant delimiter; and
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
182 (3) features in columns and samples in rows.
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
183
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
184 Downstream Tools
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
185 +---------+--------------+----------------------+
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
186 | Name | Output File | Format |
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
187 +=========+==============+======================+
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
188 | matchMS | Mass Spectra | collection (tgz/msp) |
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
189 +---------+--------------+----------------------+
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
190
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
191 @GENERAL_HELP@
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
192 </help>
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
193
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
194 <expand macro="citations" />
cb0b83b330fd "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/ramclustr commit c69f8d9772bdb9fb3cc9473651397cd6bb877020"
recetox
parents:
diff changeset
195 </tool>