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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 9bc547872c98a9c13c561d15e8990fe82bdc0e72"
author recetox
date Fri, 28 Jan 2022 16:27:04 +0000
parents b8b1b865c82d
children
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c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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1 <tool id="recetox_xmsannotator_simple" name="RECETOX xMSannotator simple" version="@TOOL_VERSION@+galaxy0">
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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2 <description>annotate peak intensity table</description>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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3 <macros>
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4 <import>macros.xml</import>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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5 </macros>
3
b8b1b865c82d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit 2c173d0e31d016311ee2d73c468818b776a423b4"
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6 <expand macro="creator"/>
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c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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7 <expand macro="requirements" />
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8 <command detect_errors="aggressive"><![CDATA[
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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9 Rscript $wrapper
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10 ]]></command>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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12 <configfiles>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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13 <configfile name="wrapper"><![CDATA[
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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14 library(xmsannotator)
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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16 annotation <- simple_annotation(
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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17 #if $peak_table.is_of_type("h5")
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18 peak_table = load_peak_table_hdf("${peak_table}"),
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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19 #elif $peak_table.is_of_type("parquet")
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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20 peak_table = load_peak_table_parquet("${peak_table}"),
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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21 #end if
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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22 adduct_table = load_adduct_table_parquet("${adduct_table}"),
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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23 compound_table = load_compound_table_parquet("${compound_table}"),
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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24 mass_tolerance = 1e-6 * ${mass_tolerance_ppm}
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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25 )
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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27 save_parquet(data = annotation, file = "${annotation_parquet}")
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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28 ]]></configfile>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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29 </configfiles>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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31 <inputs>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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32 <expand macro="inputs"/>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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33 <expand macro="tolerance"/>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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34 </inputs>
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c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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36 <outputs>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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37 <expand macro="outputs"/>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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38 </outputs>
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c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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40 <help>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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41 <![CDATA[
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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42 @HELP@
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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43 ]]>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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44 </help>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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46 <citations>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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47 <expand macro="citations"/>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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48 </citations>
c72233720bdc "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/recetox-xmsannotator commit e547915248546657de13b91f28e5f4488ae8f7e0"
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49 </tool>