Mercurial > repos > recetox > matchms_convert

comparison matchms_convert.xml @ 4:d4609fbf8ca3 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 b1cc1aebf796f170d93e3dd46ffcdefdc7b8018a
author recetox
date Thu, 12 Oct 2023 13:30:20 +0000
parents b9cc12600553
children c5ed6bfcd806
comparison
equal deleted inserted replaced
3:b9cc12600553 4:d4609fbf8ca3
1 <tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy0" profile="21.05"> 1 <tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy2" profile="21.05">
2 <description>convert between mass spectral library formats (.mgf/.msp/.json) using matchms</description> 2 <description>convert between mass spectral library formats (.mgf/.msp/.json) using matchms</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <import>help.xml</import> 6 <import>help.xml</import>
17 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement> 17 <requirement type="package" version="@TOOL_VERSION@">matchms</requirement>
18 </requirements> 18 </requirements>
19 19
20 <command detect_errors='aggressive'><![CDATA[ 20 <command detect_errors='aggressive'><![CDATA[
21 python ${matchms_python_cli} 21 python ${matchms_python_cli}
22 #if $output_file.output_format == "msp":
23 #if $output_file.export_style == "ms_lima":
24 &&
25 sh ${ms_lima_output}
26 #end if
27 #end if
22 ]]></command> 28 ]]></command>
23 29
24 <configfiles> 30 <configfiles>
25 <configfile name="matchms_python_cli"> 31 <configfile name="matchms_python_cli">
26 @init_logger@ 32 @init_logger@
27 33
28 from matchms.importing import load_from_msp, load_from_mgf, load_from_json 34 from matchms.importing import load_from_msp, load_from_mgf, load_from_json
29 from matchms.exporting import save_as_msp, save_as_mgf, save_as_json 35 from matchms.exporting import save_as_msp, save_as_mgf, save_as_json
30 spectra = list(load_from_${spectral_library.ext}("${spectral_library}", ${harmonization_metadata})) 36 spectra = list(load_from_${spectral_library.ext}("${spectral_library}", ${harmonization_metadata}))
31 #if $output_file.output_format == "msp" 37 #if $output_file.output_format == "msp"
38 #if $output_file.export_style == "ms_lima"
39 save_as_msp(spectra, "${converted_library}", write_peak_comments = ${output_file.export_peak_comments}, style = "riken")
40 #else
32 save_as_msp(spectra, "${converted_library}", write_peak_comments = ${output_file.export_peak_comments}, style = "${output_file.export_style}") 41 save_as_msp(spectra, "${converted_library}", write_peak_comments = ${output_file.export_peak_comments}, style = "${output_file.export_style}")
42 #end if
33 #else 43 #else
34 save_as_${output_file.output_format}(spectra, "${converted_library}") 44 save_as_${output_file.output_format}(spectra, "${converted_library}")
35 #end if 45 #end if
46 </configfile>
47 <configfile name="ms_lima_output">
48 sed -E "s,[[:space:]]+, ,g" ${converted_library} > ${converted_library}.tmp
49
50 grep -rl 'IONMODE' . | xargs sed '/IONMODE/d' ${converted_library}.tmp > ${converted_library}.tmp1
51 grep -rl 'CHARGE' . | xargs sed '/CHARGE/d' ${converted_library}.tmp1 > ${converted_library}.tmp2
52 grep -rl 'COMPOUND_NAME' . | xargs sed 's/COMPOUND_NAME/NAME/g' ${converted_library}.tmp2 > ${converted_library}.tmp3
53
54 mv ${converted_library}.tmp3 ${converted_library}
55 rm -f ${converted_library}.tmp1 ${converted_library}.tmp2 ${converted_library}.tmp3 ${converted_library}.tmp
36 </configfile> 56 </configfile>
37 </configfiles> 57 </configfiles>
38 58
39 <inputs> 59 <inputs>
40 <param label="Spectra file" name="spectral_library" type="data" format="msp,mgf,json" 60 <param label="Spectra file" name="spectral_library" type="data" format="msp,mgf,json"
60 <option value="matchms" selected="true">matchms</option> 80 <option value="matchms" selected="true">matchms</option>
61 <option value="massbank">massbank</option> 81 <option value="massbank">massbank</option>
62 <option value="nist">nist</option> 82 <option value="nist">nist</option>
63 <option value="riken">riken</option> 83 <option value="riken">riken</option>
64 <option value="gnps">gnps</option> 84 <option value="gnps">gnps</option>
85 <option value="ms_lima">ms-lima</option>
65 </param> 86 </param>
66 </when> 87 </when>
67 <when value="mgf" /> 88 <when value="mgf" />
68 <when value="json" /> 89 <when value="json" />
69 </conditional> 90 </conditional>
113 <param name="export_peak_comments" value="True"/> 134 <param name="export_peak_comments" value="True"/>
114 <param name="output_format" value="msp"/> 135 <param name="output_format" value="msp"/>
115 <param name="export_style" value="matchms"/> 136 <param name="export_style" value="matchms"/>
116 <output name="converted_library" file="convert/harmonized_msp_peakcomments_out.msp" ftype="msp"/> 137 <output name="converted_library" file="convert/harmonized_msp_peakcomments_out.msp" ftype="msp"/>
117 </test> 138 </test>
139 <test>
140 <param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
141 <param name="harmonization_metadata" value="True"/>
142 <param name="export_peak_comments" value="False"/>
143 <param name="output_format" value="msp"/>
144 <param name="export_style" value="ms_lima"/>
145 <output name="converted_library" file="convert/ms_lima_output.msp" ftype="msp"/>
146 </test>
118 </tests> 147 </tests>
119 148
120 149
121 <help><![CDATA[ 150 <help><![CDATA[
122 Description 151 Description