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author recetox
date Thu, 26 Sep 2024 13:02:58 +0000
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1 <tool id="use_theoretical_mz_annotations" name="use theoretical m/z values" version="@TOOL_VERSION@+galaxy1" profile="21.09">
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2 <description>Overwrite experimentally measured mz values for peaks with theoretical values from peak comments.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="creator"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 python3 '${__tool_directory__}/use_theoretical_mz_annotations.py'
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10 -i '${input}'
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11 -o '${output_data}'
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12 #if $only_theoretical_annotated
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13 -a
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14 #end if
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15 ]]>
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16 </command>
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18 <inputs>
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19 <param name="input" type="data" format="msp,mgf" label="Input mass spectral library with peak comments in RIKEN format." />
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20 <param name="only_theoretical_annotated" type="boolean" label="only retain annotated peaks" truevalue="True" falsevalue="False" checked="false" />
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21 </inputs>
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23 <outputs>
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24 <data name="output_data" format_source="input" />
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25 </outputs>
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27 <tests>
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28 <test>
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29 <param name="input" value="input.msp" ftype="msp"/>
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30 <param name="only_theoretical_annotated" value="True"/>
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31 <output name="output_data" value="output_only_annotated.msp"/>
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32 </test>
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33 <test>
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34 <param name="input" value="input.msp" ftype="msp"/>
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35 <param name="only_theoretical_annotated" value="False"/>
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36 <output name="output_data" value="output_plus_no_annotated.msp"/>
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37 </test>
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38 </tests>
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40 <help>
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41 <![CDATA[
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42 This tool uses theoretical M/Z annotations in the input MSP or MGF file.
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43 You can choose whether to include non-annotated peaks in the output.
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44 ]]>
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45 </help>
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46 <!-- check is this is the correct citation -->
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47 <citations>
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48 <citation type="doi">10.21105/joss.04337</citation>
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49 </citations>
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50 </tool>