Mercurial > repos > recetox > mfassignr_isofiltr

comparison mfassignr_isofiltr.xml @ 1:079ae9aa6ed5 draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/mfassignr commit 87bb82e07c57753a71d9ce4efc757c4367200d15
author recetox
date Thu, 15 Aug 2024 12:01:23 +0000
parents c12a49b04ca0
children e4ddc3bc7e15
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0:c12a49b04ca0 1:079ae9aa6ed5
1 <tool id="mfassignr_isofiltr" name="MFAssignR IsoFiltR" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="mfassignr_isofiltr" name="MFAssignR IsoFiltR" version="@TOOL_VERSION@+galaxy0" profile="23.0">
2 <description> 2 <description>Separates likely isotopic masses from monoisotopic masses in a mass list</description>
3 IsoFiltR separates likely isotopic masses from monoisotopic masses in a mass list.
4 </description>
5 <macros> 3 <macros>
6 <import>macros.xml</import> 4 <import>macros.xml</import>
7 </macros> 5 </macros>
6 <edam_topics>
7 <edam_topic>topic_3172</edam_topic>
8 </edam_topics>
9 <edam_operations>
10 <edam_operation>operation_3629</edam_operation>
11 </edam_operations>
8 <expand macro="creator" /> 12 <expand macro="creator" />
9 <expand macro="refs" /> 13 <expand macro="refs" />
10 14
11 <expand macro="requirements" /> 15 <expand macro="requirements" />
12 <command detect_errors="exit_code"><![CDATA[ 16 <command detect_errors="exit_code"><![CDATA[
13 Rscript 17 Rscript '${mfassignr_isofiltr}'
14 -e 'source("${mfassignr_isofiltr}")'
15 ]]> 18 ]]>
16 </command> 19 </command>
17 <configfiles> 20 <configfiles>
18 <configfile name="mfassignr_isofiltr"><![CDATA[ 21 <configfile name="mfassignr_isofiltr"><![CDATA[
19 peaks <- read.table("$peaks", header=TRUE, sep="\t") 22 peaks <- read.table("$peaks", header=TRUE, sep="\t")
38 <data name="iso_out" format="tabular" label="Isotopic Masses"/> 41 <data name="iso_out" format="tabular" label="Isotopic Masses"/>
39 </outputs> 42 </outputs>
40 <tests> 43 <tests>
41 <test> 44 <test>
42 <param name="peaks" value="QC1_1_POS_500.tabular" ftype="tabular"/> 45 <param name="peaks" value="QC1_1_POS_500.tabular" ftype="tabular"/>
43 <output name="mono_out" file="isofiltr_output1.tabular" ftype="tabular"/> 46 <output name="mono_out" file="isofiltr/mono_out.tabular" ftype="tabular"/>
44 <output name="iso_out" file="isofiltr_output2.tabular" ftype="tabular"/> 47 <output name="iso_out" file="isofiltr/iso_out.tabular" ftype="tabular"/>
45 </test> 48 </test>
46 </tests> 49 </tests>
47 <help> 50 <help>
48 IsoFiltR identifies and separates likely isotopic masses from monoisotopic masses in a mass list. 51 IsoFiltR identifies and separates likely isotopic masses from monoisotopic masses in a mass list.
49 This should be done prior to formula assignment to reduce incorrect formula assignments. 52 This should be done prior to formula assignment to reduce incorrect formula assignments.