Mercurial > repos > recetox > matchms_filtering

comparison matchms_filtering.xml @ 5:a177ac3c752c draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/matchms commit f79a5b51599254817727bc9028b9797ea994cb4e
author recetox
date Tue, 27 Jun 2023 14:25:01 +0000
parents 1f2b13dbc0c8
children 13de8005adba
comparison
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4:357df6c47d92 5:a177ac3c752c
1 <tool id="matchms_filtering" name="matchMS filtering" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="matchms_filtering" name="matchms filtering" version="@TOOL_VERSION@+galaxy0" profile="21.09">
2 <description>filter and normalize mass spectrometry data</description> 2 <description>filter and normalize mass spectrometry data</description>
3
3 <macros> 4 <macros>
4 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <import>help.xml</import>
5 </macros> 7 </macros>
8
6 <expand macro="creator"/> 9 <expand macro="creator"/>
10
11 <edam_operations>
12 <edam_operation>operation_3695</edam_operation>
13 </edam_operations>
14 <expand macro="bio.tools"/>
15
7 <requirements> 16 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> 17 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
9 <requirement type="package" version="1.1.4">pandas</requirement>
10 </requirements> 18 </requirements>
19
20 <command detect_errors="exit_code"><![CDATA[
21 sh ${matchms_python_cli}
22 ]]> </command>
11 23
12 <environment_variables> 24 <environment_variables>
13 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable> 25 <environment_variable name="MPLCONFIGDIR">\$_GALAXY_JOB_TMP_DIR</environment_variable>
14 </environment_variables> 26 </environment_variables>
15
16 <command detect_errors="exit_code"><![CDATA[
17 sh ${matchms_python_cli}
18 ]]> </command>
19 27
20 <configfiles> 28 <configfiles>
21 <configfile name="matchms_python_cli"> 29 <configfile name="matchms_python_cli">
22 python3 ${__tool_directory__}/matchms_filtering_wrapper.py \ 30 python3 ${__tool_directory__}/matchms_filtering_wrapper.py \
23 --spectra "$spectra" \ 31 --spectra "$spectra" \
65 73
66 <conditional name="relative_intensity"> 74 <conditional name="relative_intensity">
67 <param name="is_true" label="Filter relative intensity" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" 75 <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)." /> 76 help="Keep only peaks within set relative intensity range (keep if maximum >= intensity >= minimum)." />
69 <when value="TRUE"> 77 <when value="TRUE">
70 <param label="Minimum intensity" name="from_intensity" optional="true" type="float" help="Lower bound for intensity filter." /> 78 <param label="Minimum intensity" name="from_intensity" value="0" 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." /> 79 <param label="Maximum intensity" name="to_intensity" value="1" type="float" help="Upper bound for intensity filter." />
72 </when> 80 </when>
73 </conditional> 81 </conditional>
74 82
75 <conditional name="mz_range"> 83 <conditional name="mz_range">
76 <param name="is_true" label="Filter m/z range" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" 84 <param name="is_true" label="Filter m/z range" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false"
127 </section> 135 </section>
128 <output name="output" file="filtering/mz_range.msp" ftype="msp"/> 136 <output name="output" file="filtering/mz_range.msp" ftype="msp"/>
129 </test> 137 </test>
130 </tests> 138 </tests>
131 139
132 <help><![CDATA[ 140 <help>
133 Documentation 141 @HELP_matchms@
134 For documentation on the tool see https://github.com/matchms/matchms/blob/master/README.rst and https://matchms.readthedocs.io/en/latest/. 142 </help>
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
149 143
150 <expand macro="citations"/> 144 <expand macro="citations"/>
151 </tool> 145 </tool>