Mercurial > repos > recetox > matchms_convert
diff matchms_convert.xml @ 23:5611c132f607 draft default tip
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 |
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--- a/matchms_convert.xml Mon Jun 30 13:04:10 2025 +0000 +++ b/matchms_convert.xml Thu Aug 14 12:43:17 2025 +0000 @@ -1,4 +1,4 @@ -<tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy0" profile="23.0" license="MIT"> +<tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy2" profile="23.0" license="MIT"> <description>convert between mass spectral library formats (.mgf/.msp/.json) using matchms</description> <macros> @@ -47,12 +47,11 @@ <configfile name="ms_lima_output"> sed -E "s,[[:space:]]+, ,g" ${converted_library} > ${converted_library}.tmp -grep -rl 'IONMODE' . | xargs sed '/IONMODE/d' ${converted_library}.tmp > ${converted_library}.tmp1 -grep -rl 'CHARGE' . | xargs sed '/CHARGE/d' ${converted_library}.tmp1 > ${converted_library}.tmp2 -grep -rl 'COMPOUND_NAME' . | xargs sed 's/COMPOUND_NAME/NAME/g' ${converted_library}.tmp2 > ${converted_library}.tmp3 +grep -rl 'CHARGE' . | xargs sed '/CHARGE/d' ${converted_library}.tmp > ${converted_library}.tmp1 +grep -rl 'COMPOUND_NAME' . | xargs sed 's/COMPOUND_NAME/NAME/g' ${converted_library}.tmp1 > ${converted_library}.tmp2 -mv ${converted_library}.tmp3 ${converted_library} -rm -f ${converted_library}.tmp1 ${converted_library}.tmp2 ${converted_library}.tmp3 ${converted_library}.tmp +mv ${converted_library}.tmp2 ${converted_library} +rm -f ${converted_library}.tmp1 ${converted_library}.tmp2 ${converted_library}.tmp </configfile> </configfiles> @@ -177,7 +176,7 @@ Some of the metadata keywords might change during the conversion process, as they are harmonized internally with matchms. .. rubric:: **Footnotes** - .. [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. + .. [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. @HELP_matchms@ ]]></help>