Mercurial > repos > recetox > isolib

annotate isolib.xml @ 4:2b1118bce0b1 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/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
author recetox
date Fri, 01 Nov 2024 08:45:59 +0000
parents b3251a7dae25
children 964b4559eb1b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
1 <tool id="isolib" name="isolib" version="2.6+galaxy0" profile="21.09">
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
2 <description>create an isotopic pattern library for given compounds and adducts based on enviPat</description>
0
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
3 <creator>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
4 <person
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
5 givenName="Helge"
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
6 familyName="Hecht"
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
7 url="https://github.com/hechth"
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
8 identifier="0000-0001-6744-996X" />
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
9 <organization
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
10 url="https://www.recetox.muni.cz/"
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
11 email="GalaxyToolsDevelopmentandDeployment@space.muni.cz"
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
12 name="RECETOX MUNI" />
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
13 </creator>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
14 <edam_operations>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
15 <edam_operation>operation_3632</edam_operation>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
16 </edam_operations>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
17 <requirements>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
18 <requirement type="package" version="1.10.0">bioconductor-metabocoreutils</requirement>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
19 <requirement type="package" version="1.12.0">bioconductor-spectra</requirement>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
20 <requirement type="package" version="1.6.0">bioconductor-msbackendmsp</requirement>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
21 <requirement type="package" version="2.6">r-envipat</requirement>
2
b3251a7dae25 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit b9574494a6f9d2239dc81899e6d4074b33b078b7
recetox
parents: 1
diff changeset
22 <requirement type="package" version="2.1.5">r-readr</requirement>
4
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
23 <requirement type="package" version="1.3.1">r-tidyr</requirement>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
24 <requirement type="package" version="1.5.1">r-stringr</requirement>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
25 <requirement type="package" version="1.0.2">r-purrr</requirement>
0
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
26 </requirements>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
27 <command detect_errors="exit_code"><![CDATA[
4
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
28 Rscript '${__tool_directory__}/isolib.R'
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
29 '${input_file}'
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
30 '${ionization.adducts}'
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
31 '${threshold}'
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
32 '${append_adduct}'
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
33 #if $formatting.out_format == "tabular"
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
34 '${formatting.append_isotopes}'
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
35 #else
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
36 'FALSE'
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
37 #end if
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
38 '${formatting.out_format}'
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
39 '${isotope_library}'
0
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
40 ]]></command>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
41 <inputs>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
42 <param name="input_file" type="data" format="tabular" label="Table with input compounds"/>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
43 <conditional name="ionization">
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
44 <param name="ionization" type="select" label="Ionization mode" help="Ionization mode used in the experiment">
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
45 <option value="negative" selected="true">negative</option>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
46 <option value="positive">positive</option>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
47 </param>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
48 <when value="positive">
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
49 <param name="adducts" type="select" label="Adducts" multiple="true" help="Adducts to use">
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
50 <option value="M+H" selected="true">M+H</option>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
51 </param>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
52 </when>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
53 <when value="negative">
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
54 <param name="adducts" type="select" label="Adducts" multiple="true" help="Adducts to use">
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
55 <option value="M-H" selected="true">M-H</option>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
56 <option value="M-2H">M-2H</option>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
57 <option value="2M-H">2M-H</option>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
58 </param>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
59 </when>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
60 </conditional>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
61 <param name="threshold" type="float" min="0" max="100" value="1" label="Threshold" help="Probability threshold to use as cutoff for isotopic pattern distribution - this can be used to remove low abundant peaks and improve computation performance." />
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
62 <param name="append_adduct" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" label="Append adduct to compound name" help="Append the adduct string to the compound name for easy identification." />
4
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
63 <conditional name="formatting">
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
64 <param name="out_format" type="select" label="Output Format" help="Choose the output format, either MSP or Tabular">
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
65 <option value="tabular">tabular</option>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
66 <option value="msp" selected="true">msp</option>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
67 </param>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
68 <when value="tabular">
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
69 <param name="append_isotopes" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Append isotopes to formula" help="Append the isotopic composition to the formula for easy identification." />
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
70 </when>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
71 <when value="msp">
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
72 </when>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
73 </conditional>
0
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
74 </inputs>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
75 <outputs>
4
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
76 <data format="msp" name="isotope_library">
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
77 <change_format>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
78 <when input="formatting.out_format" value="msp" format="msp" />
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
79 <when input="formatting.out_format" value="tabular" format="tabular" />
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
80 </change_format>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
81 </data>
0
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
82 </outputs>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
83
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
84 <tests>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
85 <test>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
86 <param name="input_file" value="lc_markers_neg.tsv"/>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
87 <output name="isotope_library" file="test0.msp"/>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
88 </test>
2
b3251a7dae25 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit b9574494a6f9d2239dc81899e6d4074b33b078b7
recetox
parents: 1
diff changeset
89 <test>
b3251a7dae25 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit b9574494a6f9d2239dc81899e6d4074b33b078b7
recetox
parents: 1
diff changeset
90 <param name="input_file" value="markers_no_rt.tsv"/>
b3251a7dae25 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit b9574494a6f9d2239dc81899e6d4074b33b078b7
recetox
parents: 1
diff changeset
91 <output name="isotope_library" file="test1.msp"/>
b3251a7dae25 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit b9574494a6f9d2239dc81899e6d4074b33b078b7
recetox
parents: 1
diff changeset
92 </test>
4
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
93 <test>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
94 <param name="input_file" value="lc_markers_neg.tsv"/>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
95 <param name="out_format" value="tabular"/>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
96 <param name="append_isotopes" value="TRUE" />
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
97 <output name="isotope_library" file="test2.tabular"/>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
98 </test>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
99 <test>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
100 <param name="input_file" value="lc_markers_neg.tsv"/>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
101 <param name="out_format" value="tabular"/>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
102 <param name="adducts" value="M-H,2M-H"/>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
103 <output name="isotope_library" file="test3.tabular"/>
2b1118bce0b1 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit e21ab1b7f16bc0a58b33b8e46f828e150372c307
recetox
parents: 2
diff changeset
104 </test>
0
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
105 </tests>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
106 <help><![CDATA[
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
107 This tool computes isotopic patterns for given compounds and adduct forms.
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
108 The compound table input file should contain the following columns:
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
109 - name: compound name
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
110 - formula: compound formula
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
111 - rt (optional): retention time
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
112
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
113 The output is a spectral library in the MSP format.
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
114 ]]></help>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
115 <citations>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
116 <citation type="doi">10.1021/acs.analchem.5b00941</citation>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
117 <citation type="doi">10.3390/metabo12020173</citation>
8a1893635ac0 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit 019a1087adb6bd570eada9ce1d7d6fcd6d55bff8
recetox
parents:
diff changeset
118 </citations>
1
7a4540275084 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/isolib commit aea55301f6e688afb74190346d8fd0e9b0d9ed57
recetox
parents: 0
diff changeset
119 </tool>