Mercurial > repos > recetox > matchms_filtering

annotate matchms_filtering.xml @ 13:ca5a8db023e1 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/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
author recetox
date Thu, 14 Dec 2023 13:45:58 +0000
parents 039e7ab31836
children da15e8ea3b28
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
13
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
1 <tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy1" profile="21.09">
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
2 <description>filter and normalize mass spectrometry data</description>
5
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
3
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
4 <macros>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
5 <import>macros.xml</import>
5
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
6 <import>help.xml</import>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
7 </macros>
5
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
8
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
9 <expand macro="creator"/>
5
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
10
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
11 <edam_operations>
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
12 <edam_operation>operation_3695</edam_operation>
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
13 </edam_operations>
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
14 <expand macro="bio.tools"/>
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
15
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
16 <requirements>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
17 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
18 </requirements>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
19
5
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
20 <command detect_errors="exit_code"><![CDATA[
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
21 sh ${matchms_python_cli}
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
22 ]]> </command>
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
23
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
24 <environment_variables>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
25 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
26 </environment_variables>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
27
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
28 <configfiles>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
29 <configfile name="matchms_python_cli">
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
30 python3 ${__tool_directory__}/matchms_filtering_wrapper.py \
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
31 --spectra "$spectra" \
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
32 --spectra_format "$spectra.ext" \
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
33 #if $normalise_intensities_is_true == "TRUE"
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
34 -normalise_intensities \
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
35 #end if
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
36 #if $default_filters_is_true == "TRUE"
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
37 -default_filters \
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
38 #end if
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
39 #if $clean_metadata_is_true == "TRUE"
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
40 -clean_metadata \
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
41 #end if
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
42 #if $relative_intensity.is_true == "TRUE"
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
43 -relative_intensity \
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
44 --from_intensity "$relative_intensity.from_intensity" \
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
45 --to_intensity "$relative_intensity.to_intensity" \
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
46 #end if
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
47 #if $mz_range.is_true == "TRUE"
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
48 -mz_range \
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
49 --from_mz "$mz_range.from_mz" \
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
50 --to_mz "$mz_range.to_mz" \
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
51 #end if
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
52 #if $require_smiles_is_true == "TRUE"
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
53 -require_smiles \
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
54 #end if
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
55 #if $require_inchi_is_true == "TRUE"
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
56 -require_inchi \
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
57 #end if
13
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
58 #if $derive_precursor_mz_from_parent_mass.is_true == "TRUE"
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
59 -derive_precursor_mz_from_parent_mass \
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
60 --estimate_from_adduct "${derive_precursor_mz_from_parent_mass.estimate_from_adduct}" \
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
61 #end if
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
62 #if $reduce_to_top_n_peaks.is_true == "TRUE"
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
63 -reduce_to_top_n_peaks \
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
64 --n_max "$reduce_to_top_n_peaks.n_max" \
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
65 #end if
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
66 --output "$output"
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
67 </configfile>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
68 </configfiles>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
69
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
70 <inputs>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
71 <param label="Spectra file" name="spectra" type="data" format="msp,mgf" help="Mass spectra file to be filtered." />
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
72 <param name="normalise_intensities_is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
73 help="Normalize intensities of peaks (and losses) to unit height."/>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
74 <param name="default_filters_is_true" label="Apply default filters" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
75 help="Collection of filters that are considered default and that do no require any (factory) arguments."/>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
76 <param name="clean_metadata_is_true" label="Clean metadata" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
77 help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata." />
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
78
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
79 <conditional name="relative_intensity">
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
80 <param name="is_true" label="Filter relative intensity" type="select"
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
81 help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum).">
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
82 <option value="FALSE" selected="true">FALSE</option>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
83 <option value="TRUE">TRUE</option>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
84 </param>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
85 <when value="TRUE">
5
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
86 <param label="Minimum intensity" name="from_intensity" value="0" type="float" help="Lower bound for intensity filter." />
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
87 <param label="Maximum intensity" name="to_intensity" value="1" type="float" help="Upper bound for intensity filter." />
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
88 </when>
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
89 <when value="FALSE"></when>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
90 </conditional>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
91
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
92 <conditional name="mz_range">
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
93 <param name="is_true" label="Filter m/z range" type="select"
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
94 help="Keep only peaks between set m/z range (keep if maximum >= m/z >= minimum).">
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
95 <option value="FALSE" selected="true">FALSE</option>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
96 <option value="TRUE">TRUE</option>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
97 </param>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
98 <when value="TRUE">
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
99 <param label="Minimum m/z" name="from_mz" optional="true" type="float" help="Lower bound for m/z filter." />
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
100 <param label="Maximum m/z" name="to_mz" optional="true" type="float" help="Upper bound for m/z filter." />
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
101 </when>
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
102 <when value="FALSE"></when>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
103 </conditional>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
104
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
105 <param name="require_smiles_is_true" label="Require SMILES" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
106 help="Remove spectra that does not contain SMILES." />
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
107
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
108 <param name="require_inchi_is_true" label="Require INCHI" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
109 help="Remove spectra that does not contain INCHI." />
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
110
13
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
111 <conditional name="derive_precursor_mz_from_parent_mass">
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
112 <param name="is_true" label="Derive precursor_mz from parent_mass" type="select"
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
113 help="Derives the precursor_mz from the parent mass and adduct or charge.">
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
114 <option value="FALSE" selected="true">FALSE</option>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
115 <option value="TRUE">TRUE</option>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
116 </param>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
117 <when value="TRUE">
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
118 <param label="Estimate from adduct" name="estimate_from_adduct" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" />
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
119 </when>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
120 <when value="FALSE"></when>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
121 </conditional>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
122
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
123 <conditional name="reduce_to_top_n_peaks">
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
124 <param name="is_true" label="Reduce to top n peaks" type="select"
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
125 help="Lowest intensity peaks will be removed when it has more peaks than desired.">
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
126 <option value="FALSE" selected="true">FALSE</option>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
127 <option value="TRUE">TRUE</option>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
128 </param>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
129 <when value="TRUE">
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
130 <param label="Maximum number of peaks" name="n_max" value="5" type="integer" help="Maximum number of peaks. Remove peaks if more peaks are found." />
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
131 </when>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
132 <when value="FALSE"></when>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
133 </conditional>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
134
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
135 </inputs>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
136
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
137 <outputs>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
138 <data label="${tool.name} on ${on_string}" name="output" format_source="spectra" />
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
139 </outputs>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
140
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
141 <tests>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
142 <test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
143 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
144 <param name="normalise_intensities_is_true" value="TRUE"/>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
145 <output name="output" file="filtering/normalise_intensities.msp" ftype="msp"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
146 </test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
147 <test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
148 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
149 <param name="default_filters_is_true" value="TRUE"/>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
150 <output name="output" file="filtering/default_filters.msp" ftype="msp"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
151 </test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
152 <test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
153 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
154 <param name="clean_metadata_is_true" value="TRUE"/>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
155 <output name="output" file="filtering/clean_metadata.msp" ftype="msp"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
156 </test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
157 <test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
158 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
159 <section name="relative_intensity">
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
160 <param name="is_true" value="TRUE"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
161 <param name="from_intensity" value="0.3"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
162 <param name="to_intensity" value="0.9"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
163 </section>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
164 <output name="output" file="filtering/relative_intensity.msp" ftype="msp"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
165 </test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
166 <test>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
167 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
168 <section name="mz_range">
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
169 <param name="is_true" value="TRUE"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
170 <param name="from_mz" value="300"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
171 <param name="to_mz" value="800"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
172 </section>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
173 <output name="output" file="filtering/mz_range.msp" ftype="msp"/>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
174 </test>
6
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
175 <test>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
176 <param name="spectra" value="filtering/require_filter.msp" ftype="msp"/>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
177 <param name="require_smiles_is_true" value="TRUE"/>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
178 <output name="output" file="filtering/require_smiles_out.msp" ftype="msp"/>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
179 </test>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
180 <test>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
181 <param name="spectra" value="filtering/require_filter.msp" ftype="msp"/>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
182 <param name="require_inchi_is_true" value="TRUE"/>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
183 <output name="output" file="filtering/require_inchi_out.msp" ftype="msp"/>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
184 </test>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
185 <test>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
186 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
187 <section name="reduce_to_top_n_peaks">
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
188 <param name="is_true" value="TRUE"/>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
189 <param name="n_max" value="5"/>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
190 </section>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
191 <output name="output" file="filtering/reduce_to_top_n_peaks.msp" ftype="msp"/>
13de8005adba planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
recetox
parents: 5
diff changeset
192 </test>
13
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
193 <test>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
194 <param name="spectra" value="filtering/derive_precursor_mz.msp" ftype="msp"/>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
195 <section name="derive_precursor_mz_from_parent_mass">
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
196 <param name="is_true" value="TRUE"/>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
197 <param name="estimate_from_adduct" value="TRUE"/>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
198 </section>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
199 <output name="output" file="filtering/derive_precursor_mz_out.msp" ftype="msp"/>
ca5a8db023e1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 98223db312c30b0e121a1422a9534a3db3fbf0c0
recetox
parents: 7
diff changeset
200 </test>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
201 </tests>
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
202
5
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
203 <help>
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
204 @HELP_matchms@
a177ac3c752c planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
recetox
parents: 3
diff changeset
205 </help>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
206
3
1f2b13dbc0c8 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f7bab98744e338dcdbdc9cf6f9de287632c76ea2
recetox
parents: 2
diff changeset
207 <expand macro="citations"/>
0
3d275fbdf741 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
recetox
parents:
diff changeset
208 </tool>