Mercurial > repos > recetox > matchms_convert

comparison matchms_convert.xml @ 23:5611c132f607 draft default tip

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 a57d984a9850c1faa44b6948981eb1303881ba9c
author recetox
date Thu, 14 Aug 2025 12:43:17 +0000
parents 50836782d36f
children
comparison
equal deleted inserted replaced
22:50836782d36f 23:5611c132f607
1 <tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy0" profile="23.0" license="MIT"> 1 <tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy2" profile="23.0" license="MIT">
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>
45 #end if 45 #end if
46 </configfile> 46 </configfile>
47 <configfile name="ms_lima_output"> 47 <configfile name="ms_lima_output">
48 sed -E "s,[[:space:]]+, ,g" ${converted_library} > ${converted_library}.tmp 48 sed -E "s,[[:space:]]+, ,g" ${converted_library} > ${converted_library}.tmp
49 49
50 grep -rl 'IONMODE' . | xargs sed '/IONMODE/d' ${converted_library}.tmp > ${converted_library}.tmp1 50 grep -rl 'CHARGE' . | xargs sed '/CHARGE/d' ${converted_library}.tmp > ${converted_library}.tmp1
51 grep -rl 'CHARGE' . | xargs sed '/CHARGE/d' ${converted_library}.tmp1 > ${converted_library}.tmp2 51 grep -rl 'COMPOUND_NAME' . | xargs sed 's/COMPOUND_NAME/NAME/g' ${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 52
54 mv ${converted_library}.tmp3 ${converted_library} 53 mv ${converted_library}.tmp2 ${converted_library}
55 rm -f ${converted_library}.tmp1 ${converted_library}.tmp2 ${converted_library}.tmp3 ${converted_library}.tmp 54 rm -f ${converted_library}.tmp1 ${converted_library}.tmp2 ${converted_library}.tmp
56 </configfile> 55 </configfile>
57 </configfiles> 56 </configfiles>
58 57
59 <inputs> 58 <inputs>
60 <param label="Spectra file" name="spectral_library" type="data" format="msp,mgf,json" 59 <param label="Spectra file" name="spectral_library" type="data" format="msp,mgf,json"
175 Mass spectral libraries are often stored in various formats, such as `msp`, `mgf` or `json`. 174 Mass spectral libraries are often stored in various formats, such as `msp`, `mgf` or `json`.
176 This tool can be used to convert from one library format to another. 175 This tool can be used to convert from one library format to another.
177 Some of the metadata keywords might change during the conversion process, as they are harmonized internally with matchms. 176 Some of the metadata keywords might change during the conversion process, as they are harmonized internally with matchms.
178 177
179 .. rubric:: **Footnotes** 178 .. rubric:: **Footnotes**
180 .. [1] Export styles - see this `table <https://github.com/matchms/matchms/blob/master/matchms/data/export_key_conversions.csv>`_ for supported key conversions and detailed description of the export styles. 179 .. [1] Export styles - see the 'export\_key\_conversions' file in the matchms GitHub repository for supported key conversions and detailed description of the export styles.
181 180
182 @HELP_matchms@ 181 @HELP_matchms@
183 ]]></help> 182 ]]></help>
184 183
185 184