Mercurial > repos > lecorguille > xcms_plot_chromatogram

comparison xcms_plot_chromatogram.xml @ 2:e6fdadaf039e draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
author lecorguille
date Tue, 03 Apr 2018 11:37:40 -0400
parents fe1f0f16d9e6
children e0b5c547925d
comparison
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1:86ff4497b871 2:e6fdadaf039e
1 <tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@WRAPPER_VERSION@.0"> 1 <tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@WRAPPER_VERSION@.0">
2 <description>Plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience</description> 2 <description>Plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from MSnbase or xcms experience(s)</description>
3 3
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 <import>macros_xcms.xml</import>
6 </macros> 7 </macros>
7 8
8 <expand macro="requirements"/> 9 <expand macro="requirements"/>
9 <expand macro="stdio"/> 10 <expand macro="stdio"/>
10 11
11 <command><![CDATA[ 12 <command><![CDATA[
12 @COMMAND_XCMS_SCRIPT@/xcms_plot_chromatogram.r 13 @COMMAND_RSCRIPT@//xcms_plot_chromatogram.r
13 14
14 image '$image' 15 images 'c("${"\",\"".join(map(str, $images))}")'
16
17 #if str($sampleMetadata) != 'None':
18 sampleMetadata '$sampleMetadata'
19 #end if
15 20
16 @COMMAND_FILE_LOAD@ 21 @COMMAND_FILE_LOAD@
17 ]]></command> 22 ]]></command>
18 23
19 <inputs> 24 <inputs>
20 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" /> 25 <param name="images" type="data" format="rdata.msnbase.raw,rdata.xcms.findchrompeaks,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" multiple="true" />
26 <param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="must contain at least one column with the sample id and one column with the sample class"/>
21 27
22 <expand macro="input_file_load"/> 28 <expand macro="input_file_load"/>
23 </inputs> 29 </inputs>
24 30
25 <outputs> 31 <outputs>
26 <data name="ticsPdf" format="pdf" label="${image.name[:-6]}.TICs.pdf" from_work_dir="TICs.pdf"/> 32 <data name="ticsPdf" format="pdf" label="TICs.pdf" from_work_dir="TICs.pdf"/>
27 <data name="bpisPdf" format="pdf" label="${image.name[:-6]}.BPIs.pdf" from_work_dir="BPIs.pdf" /> 33 <data name="bpisPdf" format="pdf" label="BPIs.pdf" from_work_dir="BPIs.pdf" />
28 </outputs> 34 </outputs>
29 35
30 <tests> 36 <tests>
31 <test> 37 <test>
32 <param name="image" value="faahKO-single.xset.merged.group.retcor.RData"/> 38 <param name="images" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/>
33 <expand macro="test_file_load_single"/> 39 <expand macro="test_file_load_single"/>
34 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" /> 40 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
35 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" /> 41 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
36 </test> 42 </test>
43 <!-- DISABLE FOR TRAVIS
44 <test>
45 <param name="images" value="ko15-raw.RData,ko16-raw.RData,wt15-raw.RData,wt16-raw.RData" ftype="rdata"/>
46 <expand macro="test_file_load_single"/>
47 <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
48 <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
49 </test>
50 -->
37 </tests> 51 </tests>
38 52
39 <help><![CDATA[ 53 <help><![CDATA[
40 54
41 @HELP_AUTHORS@ 55 @HELP_AUTHORS@
55 Workflow position 69 Workflow position
56 ----------------- 70 -----------------
57 71
58 **Upstream tools** 72 **Upstream tools**
59 73
60 ========================= ================= =================== ========== 74 ========================= ================= ============================== ==========
61 Name output file format parameter 75 Name output file format parameter
62 ========================= ================= =================== ========== 76 ========================= ================= ============================== ==========
63 xcms.xcmsSet xset.RData rdata.xcms.raw RData file 77 MSnbase readMSData raw.RData rdata.msnbase.raw RData file
64 ------------------------- ----------------- ------------------- ---------- 78 ------------------------- ----------------- ------------------------------ ----------
65 xcms.retcor xset.RData rdata.xcms.retcor RData file 79 xcms.xcmsSet xset.RData rdata.xcms.findchrompeaks RData file
66 ========================= ================= =================== ========== 80 ------------------------- ----------------- ------------------------------ ----------
81 xcms.retcor xset.RData rdata.xcms.retcor RData file
82 ========================= ================= ============================== ==========
67 83
68 .. image:: xcms_plot_chromatogram_workflow.png 84 .. image:: xcms_plot_chromatogram_workflow.png
69 85
86 ---------------------------------------------------
70 87
71 ------------ 88 ------------
72 Output files 89 Output files
73 ------------ 90 ------------
74 91
83 Changelog/News 100 Changelog/News
84 -------------- 101 --------------
85 102
86 **Version 3.0.0.0 - 07/03/2018** 103 **Version 3.0.0.0 - 07/03/2018**
87 104
88 - NEW: This new tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience. It will replace the one created by xcmsSet and retcor tools. 105 - 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.
89 106
90 ]]></help> 107 ]]></help>
91 108
92 <expand macro="citation" /> 109 <expand macro="citation" />
93 </tool> 110 </tool>