Mercurial > repos > lecorguille > xcms_export_samplemetadata

comparison xcms_export_samplemetadata.xml @ 0:e3c06320f884 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 67da3bb19bde72d5e78397e5627c176896234f86
author lecorguille
date Tue, 09 Oct 2018 12:50:47 -0400
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children 8c62030a1136
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-1:000000000000 0:e3c06320f884
1 <tool id="xcms_export_samplemetadata" name="xcms get a sampleMetadata file" version="@WRAPPER_VERSION@.0">
2 <description>which need to be filled with extra information</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_export_samplemetadata.r
14
15 images 'c("${"\",\"".join(map(str, $images))}")'
16 ]]></command>
17
18 <inputs>
19 <param name="images" type="data" format="rdata.xcms.findchrompeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from multiple findChromPeaks" multiple="true" />
20 </inputs>
21
22 <outputs>
23 <data name="sampleMetadataOutput" format="tabular" label="sampleMetadata.tsv" from_work_dir="sampleMetadata.tsv" />
24 </outputs>
25
26 <tests>
27 <test>
28 <param name="images" value="ko15-xset.RData,ko16-xset.RData,wt15-xset.RData,wt16-xset.RData" ftype="rdata"/>
29 <output name="sampleMetadataOutput" file="noclass.merged.sampleMetadata.tsv" />
30 </test>
31 </tests>
32
33 <help><![CDATA[
34
35 @HELP_AUTHORS@
36
37 =======================
38 xcms get sampleMetadata
39 =======================
40
41 -----------
42 Description
43 -----------
44
45 This tool generates a skeleton of sampleMetadata with perhaps some strange sample names which are definitely compatible with xcms and R
46
47 This sampleMetadata file have to be filled with extra information as the class, batch information and maybe conditions
48
49 -----------------
50 Workflow position
51 -----------------
52
53 **Upstream tools**
54
55 ========================= ===================== ==============================
56 Name Output file Format
57 ========================= ===================== ==============================
58 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
59 ------------------------- --------------------- ------------------------------
60 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
61 ------------------------- --------------------- ------------------------------
62 xcms.findChromPeaks ``*``.raw.xset.RData rdata.xcms.findchrompeaks
63 ------------------------- --------------------- ------------------------------
64 ... ... ...
65 ========================= ===================== ==============================
66
67
68 **Downstream tools**
69
70 =========================== ==================== ============================
71 Name Output file Format
72 =========================== ==================== ============================
73 xcms.findChromPeaks Merger sampleMetadata.tsv tabular
74 =========================== ==================== ============================
75
76 .. image:: xcms_merge_workflow.png
77
78 -----------
79 Input files
80 -----------
81
82 =========================== ==================================
83 Parameter : num + label Format
84 =========================== ==================================
85 1 : RData file rdata.xcms.findchrompeaks
86 --------------------------- ----------------------------------
87 2 : RData file rdata.xcms.findchrompeaks
88 --------------------------- ----------------------------------
89 N : RData file rdata.xcms.findchrompeaks
90 =========================== ==================================
91
92
93
94
95 ------------
96 Output files
97 ------------
98
99 Example of a sampleMetadata:
100
101 =========================== ============
102 sample_name class
103 =========================== ============
104 HU_neg_028 bio
105 --------------------------- ------------
106 HU_neg_034 bio
107 --------------------------- ------------
108 Blanc04 blank
109 --------------------------- ------------
110 Blanc06 blank
111 --------------------------- ------------
112 Blanc09 blank
113 =========================== ============
114
115 ---------------------------------------------------
116
117 Changelog/News
118 --------------
119
120 **Version 3.0.0.0 - 09/10/2018**
121
122 - NEW: a new tool to generate a sampleMetadata file you will be able to complete
123
124 ]]></help>
125
126 <expand macro="citation" />
127 </tool>