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comparison track_rt_raw.xml @ 4:a8d243fcf676 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 9ea2ca0892fa55c21491c93afba790e8d9427e01-dirty
author tomnl
date Wed, 04 Apr 2018 16:34:45 -0400
parents e2635fa802bd
children
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3:31c68f2d97b5 4:a8d243fcf676
1 <tool id="track_rt_raw" name="track_rt_raw" version="0.0.8"> 1 <tool id="track_rt_raw" name="track_rt_raw" version="0.0.9">
2
3 <requirements>
4 <requirement type="package" version="1.46.0" >bioconductor-xcms</requirement>
5 </requirements>
6
7 <description>Track the raw retention time in the peak slot of XCMSset objects. 2 <description>Track the raw retention time in the peak slot of XCMSset objects.
8 </description> 3 </description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7
8 <expand macro="requirements">
9 </expand>
10
11
9 <stdio> 12 <stdio>
10 <exit_code range="1:" /> 13 <exit_code range="1:" />
11 </stdio> 14 </stdio>
12 <command interpreter="Rscript"><![CDATA[ 15 <command interpreter="Rscript"><![CDATA[
13 track_rt_raw.R 16 track_rt_raw.R
14 --xset_path=$xset 17 --xset_path=$xset
15 --out_dir=. 18 --out_dir=.
19 #if $extract_peaks:
20 --extract_peaks
21 #end if
16 22
17 ]]></command> 23 ]]></command>
18 <inputs> 24 <inputs>
19 25
20 <param type="data" name="xset" 26 <param type="data" name="xset" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.fillpeaks,rdata"
21 help="xcmsSet object saved as an RData file"/> 27 help="xcmsSet object saved as an RData file"/>
28
29 <param name="extract_peaks" type="boolean" checked="false" label="Save peaks to a tsv file"
30 />
22 31
23 </inputs> 32 </inputs>
24 <outputs> 33 <outputs>
25 34
26 <data name="xset_with_rt_raw" format="rdata" label="xset.track_rt_raw.RData" 35 <data name="xset_with_rt_raw" format="rdata" label="xset.track_rt_raw.RData" from_work_dir="xset_rt_raw_tracked.RData"/>
27 from_work_dir="xset_rt_raw_tracked.RData" visible="true"/> 36
37 <data name="xset_extract_peaks" format="tsv" label="xset_peaks.tsv" from_work_dir="xset_peaks.tsv">
38 <filter>extract_peaks is True</filter>
39 </data>
28 </outputs> 40 </outputs>
29 <tests> 41 <tests>
42 <test>
43 <param name="xset" value="LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.xset.group.rdata"/>
44 <param name="extract_peaks" value="True"/>
45 <output name="xset_extract_peaks" value="xset_peaks.tsv"/>
46 </test>
47 </tests>
30 48
31 </tests> 49
32 <help><![CDATA[]]></help> 50 <help><![CDATA[
51 =============================================================
52 Track raw retention time for XCMS set
53 =============================================================
54 -----------
55 Description
56 -----------
57 Tool to store the original raw peak information on the xset@peaks slot. Note: This can only be done BEFORE the retention alignment has been performed.
58
59
60 -----------
61 Outputs
62 -----------
63
64 * xset_with_rt_raw: xcmsSet object with raw retention of peaks saved on the xset@peaks slot
65
66
67
68 ]]></help>
69 <expand macro="citations" />
33 </tool> 70 </tool>