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comparison xcms_plot_chromatogram.xml @ 0:c749bfd3410e draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
author lecorguille
date Tue, 18 Sep 2018 16:06:05 -0400
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children 7c0cc7a3c3db
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-1:000000000000 0:c749bfd3410e
1 <tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@WRAPPER_VERSION@.0">
2 <description>Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s)</description>
3
4 <macros>
5 <import>macros.xml</import>
6 <import>macros_xcms.xml</import>
7 </macros>
8
9 <expand macro="requirements"/>
10 <expand macro="stdio"/>
11
12 <command><![CDATA[
13 @COMMAND_RSCRIPT@//xcms_plot_chromatogram.r
14
15 images 'c("${"\",\"".join(map(str, $images))}")'
16
17 #if str($sampleMetadata) != 'None':
18 sampleMetadata '$sampleMetadata'
19 #end if
20
21 @COMMAND_FILE_LOAD@
22 ]]></command>
23
24 <inputs>
25 <param name="images" type="data" format="rdata.msnbase.raw,rdata.xcms.findchrompeaks,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" multiple="true" />
26 <param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="Must contain at least one column with the sample id and one column with the sample class"/>
27
28 <expand macro="input_file_load"/>
29 </inputs>
30
31 <outputs>
32 <data name="ticsPdf" format="pdf" label="TICs.pdf" from_work_dir="TICs.pdf"/>
33 <data name="bpisPdf" format="pdf" label="BPIs.pdf" from_work_dir="BPIs.pdf" />
34 </outputs>
35
36 <tests>
37 <test>
38 <param name="images" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/>
39 <expand macro="test_file_load_single"/>
40 <param name="sampleMetadata" value="sampleMetadata.tab" ftype="tabular"/>
41 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
42 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
43 </test>
44 <!-- DISABLE FOR TRAVIS
45 <test>
46 <param name="images" value="ko15-raw.RData,ko16-raw.RData,wt15-raw.RData,wt16-raw.RData" ftype="rdata"/>
47 <expand macro="test_file_load_single"/>
48 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
49 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
50 </test>
51 -->
52 </tests>
53
54 <help><![CDATA[
55
56 @HELP_AUTHORS@
57
58 ======================
59 xcms plot chromatogram
60 ======================
61
62 -----------
63 Description
64 -----------
65
66 This tool will plot Base Peak Intensity chromatogram (BPI) and Total Ion Current chromatogram (TIC) from xcms experiments.
67
68
69 -----------------
70 Workflow position
71 -----------------
72
73 **Upstream tools**
74
75 =========================== ======================== ==============================
76 Name Output file Format
77 =========================== ======================== ==============================
78 MSnbase.readMSData ``*``.raw.RData rdata.msnbase.raw
79 --------------------------- ------------------------ ------------------------------
80 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
81 --------------------------- ------------------------ ------------------------------
82 xcms.findChromPeaks Merger xset.merged.RData rdata.xcms.retcor
83 --------------------------- ------------------------ ------------------------------
84 xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor
85 =========================== ======================== ==============================
86
87 .. image:: xcms_plot_chromatogram_workflow.png
88
89 ---------------------------------------------------
90
91 ------------
92 Output files
93 ------------
94
95 **Total Ion Current (TIC) chromatogram**
96 | Sum of intensity (Y) of all ions detected at each retention time (X)
97
98 **Base Peak Intensity Chromatogram (BPI)**
99 | Sum of intensity (Y) of the most intense peaks at each retention time (X)
100
101 ---------------------------------------------------
102
103 Changelog/News
104 --------------
105
106 **Version 3.0.0.0 - 07/03/2018**
107
108 - NEW: This new tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience. It will replace those created by xcmsSet and retcor tools.
109
110 ]]></help>
111
112 <expand macro="citation" />
113 </tool>