Mercurial > repos > recetox > xmsannotator_simple

annotate xmsannotator_simple.xml @ 3:412d8bb4b54d draft

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"planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
author recetox
date Mon, 14 Dec 2020 03:33:21 +0000
parents 041052875af0
children cd0729b7c3dc
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412d8bb4b54d "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 339f3b1b1243f353dd3ed115ac66320fdd2d2b68"
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1 <tool id="xmsannotator_simple" name="xMSannotator (simple)" version="@TOOL_VERSION@+galaxy2">
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2 <macros>
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3 <import>xmsannotator_macros.xml</import>
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4 </macros>
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6 <requirements>
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7 <container type="docker">@DOCKER_IMAGE@</container>
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8 </requirements>
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97d1619ff23e "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/xmsannotator commit 9c62378416ff3634935e7da4aa97b05d3356d1b5"
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10 <command detect_errors="aggressive"><![CDATA[
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11 Rscript $wrapper
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12 ]]></command>
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14 <configfiles>
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15 <configfile name="wrapper"><![CDATA[
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16 library(xmsannotator)
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18 annotation <- simple_annotation(
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19 #if $peak_table.is_of_type("h5")
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20 peak_table = load_peak_table_hdf("${peak_table}"),
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21 #elif $peak_table.is_of_type("parquet")
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22 peak_table = load_peak_table_parquet("${peak_table}"),
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23 #end if
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24 adduct_table = load_adduct_table_parquet("${adduct_table}"),
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25 compound_table = load_compound_table_parquet("${compound_table}"),
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26 mass_tolerance = 1e-6 * ${mass_tolerance_ppm}
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27 )
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29 save_parquet(data = annotation, file = "${annotation_parquet}")
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30 ]]></configfile>
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31 </configfiles>
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33 <inputs>
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34 <expand macro="inputs"/>
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35 <expand macro="tolerance"/>
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36 </inputs>
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38 <outputs>
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39 <expand macro="outputs"/>
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40 </outputs>
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42 <help><![CDATA[
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43 Annotate the peak intensity table (such as outputted from apLCMS) with compounds from the compounds database.
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45 The annotation process generates all possible compound-adduct pairs and matches those pairs to the measured
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46 peaks. A compound-adduct pair is pronounced as a match to a certain peak when the difference of their masses are
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47 withing some tolerance.
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48 ]]></help>
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50 <citations>
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51 <expand macro="citations"/>
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52 </citations>
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53 </tool>