Mercurial > repos > recetox > mfassignr_snplot

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 7d98b78ae27b24ee581d40ff0b624d7ecb288030
author recetox
date Fri, 01 Nov 2024 08:18:37 +0000
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5f4b3130272e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 4bd188e61f09431c0b7e73b35fb8ccf5ee7af6ac
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1 <tool id="mfassignr_snplot" name="MFAssignR SNplot" version="@TOOL_VERSION@+galaxy1" profile="23.0">
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2 <description>Noise level assessment using the SNplot function.</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>help.xml</import>
6a34bc7afd61 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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6 </macros>
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7 <edam_topics>
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8 <edam_topic>topic_3172</edam_topic>
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9 </edam_topics>
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10 <expand macro="creator"/>
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11 <expand macro="requirements" />
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12 <command detect_errors="exit_code"><![CDATA[
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13 Rscript '${run_script}'
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14 ]]></command>
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15 <configfiles>
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16 <configfile name="run_script"><![CDATA[
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17 cut = $sn_ratio * $kmdn
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18
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19 SNplot <- MFAssignR::SNplot(
6a34bc7afd61 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
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20 df = read.delim("$input_file", sep="\t"),
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21 cut = cut,
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22 mass = $mass,
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f19c0631b9e5 planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 7d98b78ae27b24ee581d40ff0b624d7ecb288030
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23 mass_window = $window_x,
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24 abundance_window = $window_y
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25 )
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27 ggplot2::ggsave(filename = "SNplot.png", SNplot)
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28 ]]></configfile>
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29 </configfiles>
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30 <inputs>
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31 <expand macro="snplot_param"/>
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32 </inputs>
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33 <outputs>
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34 <data name="SNplot" format="png" label="SNplot by ${tool.name} on ${on_string}" from_work_dir="SNplot.png"/>
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="input_file" value="QC1_1_POS_500.tabular"/>
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39 <param name="kmdn" value="549117.606606315"/>
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40 <param name="mass" value="300"/>
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41 <output name="SNplot" ftype="png" file="snplot/plot.png" />
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42 </test>
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43 </tests>
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44 <help><![CDATA[
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45 @SNPLOT_HELP@
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47 @GENERAL_HELP@
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48 ]]></help>
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49 <expand macro="citations" />
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50 </tool>