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comparison matchms_filtering.xml @ 0:3d275fbdf741 draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit 4d2ac914c951166e386a94d8ebb8cb1becfac122"
author recetox
date Tue, 22 Mar 2022 16:08:03 +0000
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-1:000000000000 0:3d275fbdf741
1 <tool id="matchms_filtering" name="matchMS filtering" version="@TOOL_VERSION@+galaxy1">
2 <description>filter and normalize mass spectrometry data</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="creator"/>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
9 <requirement type="package" version="1.1.4">pandas</requirement>
10 </requirements>
11
12 <environment_variables>
13 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
14 </environment_variables>
15
16 <command detect_errors="exit_code"><![CDATA[
17 sh ${matchms_python_cli}
18 ]]> </command>
19
20 <configfiles>
21 <configfile name="matchms_python_cli">
22 python3 ${__tool_directory__}/matchms_filtering_wrapper.py \
23 --spectra "$spectra" \
24 --spectra_format "$spectra.ext" \
25 #if $normalise_intensities.is_true
26 -normalise_intensities \
27 #end if
28 #if $default_filters.is_true
29 -default_filters \
30 #end if
31 #if $clean_metadata.is_true
32 -clean_metadata \
33 #end if
34 #if $relative_intensity.is_true
35 -relative_intensity \
36 --from_intensity "$relative_intensity.from_intensity" \
37 --to_intensity "$relative_intensity.to_intensity" \
38 #end if
39 #if $mz_range.is_true
40 -mz_range \
41 --from_mz "$mz_range.from_mz" \
42 --to_mz "$mz_range.to_mz" \
43 #end if
44 --output "$output"
45 </configfile>
46 </configfiles>
47
48 <inputs>
49 <param label="Spectra file" name="spectra" type="data" format="msp,mgf" help="Mass spectra file to be filtered." />
50
51 <conditional name="normalise_intensities">
52 <param name="is_true" label="Normalize intensities" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
53 help="Normalize intensities of peaks (and losses) to unit height."/>
54 </conditional>
55
56 <conditional name="default_filters">
57 <param name="is_true" label="Apply default filters" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
58 help="Collection of filters that are considered default and that do no require any (factory) arguments."/>
59 </conditional>
60
61 <conditional name="clean_metadata">
62 <param name="is_true" label="Clean metadata" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
63 help="Apply all adding and cleaning filters if possible, so that the spectra have canonical metadata." />
64 </conditional>
65
66 <conditional name="relative_intensity">
67 <param name="is_true" label="Filter relative intensity" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
68 help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum)." />
69 <when value="TRUE">
70 <param label="Minimum intensity" name="from_intensity" optional="true" type="float" help="Lower bound for intensity filter." />
71 <param label="Maximum intensity" name="to_intensity" optional="true" type="float" help="Upper bound for intensity filter." />
72 </when>
73 </conditional>
74
75 <conditional name="mz_range">
76 <param name="is_true" label="Filter m/z range" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
77 help="Keep only peaks between set m/z range (keep if maximum >= m/z >= minimum)." />
78 <when value="TRUE">
79 <param label="Minimum m/z" name="from_mz" optional="true" type="float" help="Lower bound for m/z filter." />
80 <param label="Maximum m/z" name="to_mz" optional="true" type="float" help="Upper bound for m/z filter." />
81 </when>
82 </conditional>
83
84 </inputs>
85
86 <outputs>
87 <data label="${tool.name} on ${on_string}" name="output" format_source="spectra" />
88 </outputs>
89
90 <tests>
91 <test>
92 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
93 <section name="normalise_intensities">
94 <param name="is_true" value="TRUE"/>
95 </section>
96 <output name="output" file="filtering/normalise_intensities.msp" ftype="msp"/>
97 </test>
98 <test>
99 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
100 <section name="default_filters">
101 <param name="is_true" value="TRUE"/>
102 </section>
103 <output name="output" file="filtering/default_filters.msp" ftype="msp"/>
104 </test>
105 <test>
106 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
107 <section name="clean_metadata">
108 <param name="is_true" value="TRUE"/>
109 </section>
110 <output name="output" file="filtering/clean_metadata.msp" ftype="msp"/>
111 </test>
112 <test>
113 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
114 <section name="relative_intensity">
115 <param name="is_true" value="TRUE"/>
116 <param name="from_intensity" value="0.3"/>
117 <param name="to_intensity" value="0.9"/>
118 </section>
119 <output name="output" file="filtering/relative_intensity.msp" ftype="msp"/>
120 </test>
121 <test>
122 <param name="spectra" value="filtering/input.msp" ftype="msp"/>
123 <section name="mz_range">
124 <param name="is_true" value="TRUE"/>
125 <param name="from_mz" value="300"/>
126 <param name="to_mz" value="800"/>
127 </section>
128 <output name="output" file="filtering/mz_range.msp" ftype="msp"/>
129 </test>
130 </tests>
131
132 <help><![CDATA[
133 Documentation
134 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst and https://matchms.readthedocs.io/en/latest/.
135
136 Upstream Tools
137 +-----------+---------------+--------+-----------+
138 | Name | Output File | Format | Parameter |
139 +===========+===============+========+===========+
140 | RAMClustR | Mass spectra | msp | references|
141 +-----------+---------------+--------+-----------+
142 | RAMClustR | Mass spectra | msp | queries |
143 +-----------+---------------+--------+-----------+
144
145 Downstream Tools
146 The output is an msp file after applying the specified filters.
147 ]]></help>
148
149
150 <citations>
151 <citation type="doi">10.5281/zenodo.4589154</citation>
152 <citation type="doi">10.21105/joss.02411</citation>
153 </citations>
154 </tool>