Mercurial > repos > recetox > mfassignr_snplot

comparison mfassignr_snplot.xml @ 4:5f4b3130272e draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 4bd188e61f09431c0b7e73b35fb8ccf5ee7af6ac
author recetox
date Mon, 21 Oct 2024 09:05:57 +0000
parents 434fa3233e96
children f19c0631b9e5
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3:ccd9b0c1aee6 4:5f4b3130272e
1 <tool id="mfassignr_snplot" name="MFAssignR SNplot" version="@TOOL_VERSION@+galaxy0" profile="23.0"> 1 <tool id="mfassignr_snplot" name="MFAssignR SNplot" version="@TOOL_VERSION@+galaxy1" profile="23.0">
2 <description>Noise level assessment using the SNplot function.</description> 2 <description>Noise level assessment using the SNplot function.</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <import>help.xml</import> 5 <import>help.xml</import>
6 </macros> 6 </macros>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 Rscript '${run_script}' 13 Rscript '${run_script}'
14 ]]></command> 14 ]]></command>
15 <configfiles> 15 <configfiles>
16 <configfile name="run_script"><![CDATA[ 16 <configfile name="run_script"><![CDATA[
17 cut = $sn_ratio * $kmdn
18
17 SNplot <- MFAssignR::SNplot( 19 SNplot <- MFAssignR::SNplot(
18 df = read.delim("$input_file", sep="\t"), 20 df = read.delim("$input_file", sep="\t"),
19 cut = $cut, 21 cut = cut,
20 mass = $mass, 22 mass = $mass,
21 window.x = $window_x, 23 window.x = $window_x,
22 window.y = $window_y 24 window.y = $window_y
23 ) 25 )
24 26
32 <data name="SNplot" format="png" label="SNplot by ${tool.name} on ${on_string}" from_work_dir="SNplot.png"/> 34 <data name="SNplot" format="png" label="SNplot by ${tool.name} on ${on_string}" from_work_dir="SNplot.png"/>
33 </outputs> 35 </outputs>
34 <tests> 36 <tests>
35 <test> 37 <test>
36 <param name="input_file" value="QC1_1_POS_500.tabular"/> 38 <param name="input_file" value="QC1_1_POS_500.tabular"/>
37 <param name="cut" value="3294705.63963789"/> 39 <param name="kmdn" value="549117.606606315"/>
38 <param name="mass" value="300"/> 40 <param name="mass" value="300"/>
39 <output name="SNplot" ftype="png" file="snplot/plot.png" /> 41 <output name="SNplot" ftype="png" file="snplot/plot.png" />
40 </test> 42 </test>
41 </tests> 43 </tests>
42 <help><![CDATA[ 44 <help><![CDATA[