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matchms convert: add MS-LIMA MSP style #408

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Oct 5, 2023
Merged

matchms convert: add MS-LIMA MSP style #408

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31 changes: 30 additions & 1 deletion tools/matchms/matchms_convert.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy0" profile="21.05">
<tool id="matchms_convert" name="matchms convert" version="@TOOL_VERSION@+galaxy1" profile="21.05">
<description>convert between mass spectral library formats (.mgf/.msp/.json) using matchms</description>

<macros>
Expand All @@ -19,6 +19,12 @@

<command detect_errors='aggressive'><![CDATA[
python ${matchms_python_cli}
#if $output_file.output_format == "msp":
#if $output_file.export_style == "ms_lima":
&&
sh ${ms_lima_output}
#end if
#end if
]]></command>

<configfiles>
Expand All @@ -29,11 +35,25 @@ from matchms.importing import load_from_msp, load_from_mgf, load_from_json
from matchms.exporting import save_as_msp, save_as_mgf, save_as_json
spectra = list(load_from_${spectral_library.ext}("${spectral_library}", ${harmonization_metadata}))
#if $output_file.output_format == "msp"
#if $output_file.export_style == "ms_lima"
save_as_msp(spectra, "${converted_library}", write_peak_comments = ${output_file.export_peak_comments}, style = "riken")
#else
save_as_msp(spectra, "${converted_library}", write_peak_comments = ${output_file.export_peak_comments}, style = "${output_file.export_style}")
#end if
#else
save_as_${output_file.output_format}(spectra, "${converted_library}")
#end if
</configfile>
<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

mv ${converted_library}.tmp3 ${converted_library}
rm -f ${converted_library}.tmp1 ${converted_library}.tmp2 ${converted_library}.tmp3 ${converted_library}.tmp
</configfile>
</configfiles>

<inputs>
Expand Down Expand Up @@ -62,6 +82,7 @@ save_as_${output_file.output_format}(spectra, "${converted_library}")
<option value="nist">nist</option>
<option value="riken">riken</option>
<option value="gnps">gnps</option>
<option value="ms_lima">ms-lima</option>
</param>
</when>
<when value="mgf" />
Expand Down Expand Up @@ -115,6 +136,14 @@ save_as_${output_file.output_format}(spectra, "${converted_library}")
<param name="export_style" value="matchms"/>
<output name="converted_library" file="convert/harmonized_msp_peakcomments_out.msp" ftype="msp"/>
</test>
<test>
<param name="spectral_library" value="convert/mgf_out.mgf" ftype="mgf"/>
<param name="harmonization_metadata" value="True"/>
<param name="export_peak_comments" value="False"/>
<param name="output_format" value="msp"/>
<param name="export_style" value="ms_lima"/>
<output name="converted_library" file="convert/ms_lima_output.msp" ftype="msp"/>
</test>
</tests>


Expand Down
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