comparison abims_xcms_summary.xml @ 32:de3b88417327 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a
author lecorguille
date Tue, 03 Apr 2018 11:40:57 -0400
parents 0b5521b78c92
children 79fe34cedc56
comparison
equal deleted inserted replaced
31:0b5521b78c92 32:de3b88417327
2 2
3 <description>Create a summary of XCMS analysis</description> 3 <description>Create a summary of XCMS analysis</description>
4 4
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 <import>macros_xcms.xml</import>
7 </macros> 8 </macros>
8 9
9 <expand macro="requirements"> 10 <expand macro="requirements">
10 <requirement type="package" version="1.32.0">bioconductor-camera</requirement> 11 <requirement type="package" version="1.32.0">bioconductor-camera</requirement>
11 </expand> 12 </expand>
12 13
13 <expand macro="stdio"/> 14 <expand macro="stdio"/>
14 15
15 <command><![CDATA[ 16 <command><![CDATA[
16 $__tool_directory__/xcms_summary.r 17 @COMMAND_RSCRIPT@/xcms_summary.r
17 18
18 image '$image' 19 image '$image'
19 htmlOutput '$htmlOutput' 20 htmlOutput '$htmlOutput'
20 user_email $__user_email__ 21 user_email $__user_email__
21 22
22 ]]></command> 23 ]]></command>
23 24
24 <inputs> 25 <inputs>
25 26
26 <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, group, retcor, fillpeaks etc.)" /> 27 <param name="image" type="data" format="rdata.xcms.findchrompeaks,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, group, retcor, fillpeaks etc.)" />
27 28
28 </inputs> 29 </inputs>
29 30
30 <outputs> 31 <outputs>
31 <data name="htmlOutput" format="html" label="xcms summary html" /> 32 <data name="htmlOutput" format="html" label="xcms summary html" />
32 </outputs> 33 </outputs>
33 34
34 <tests> 35 <tests>
35 <!--<test> 36 <!--<test>
36 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" /> 37 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" ftype="rdata"/>
37 <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" /> 38 <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" />
38 </test>--> 39 </test>-->
39 <test> 40 <test>
40 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" /> 41 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" ftype="rdata"/>
41 <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" /> 42 <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" />
42 </test> 43 </test>
43 </tests> 44 </tests>
44 45
45 <help><![CDATA[ 46 <help><![CDATA[
60 Workflow position 61 Workflow position
61 ----------------- 62 -----------------
62 63
63 **Upstream tools** 64 **Upstream tools**
64 65
65 ========================= ================= ===================== ========== 66 ========================= ================= ================================ ==========
66 Name output file format parameter 67 Name output file format parameter
67 ========================= ================= ===================== ========== 68 ========================= ================= ================================ ==========
68 xcms.xcmsSet xset.RData rdata.xcms.raw RData file 69 xcms.xcmsSet xset.RData rdata.xcms.findchrompeaks RData file
69 ------------------------- ----------------- --------------------- ---------- 70 ------------------------- ----------------- -------------------------------- ----------
70 xcms.group xset.RData rdata.xcms.group RData file 71 xcms.group xset.RData rdata.xcms.group RData file
71 ------------------------- ----------------- --------------------- ---------- 72 ------------------------- ----------------- -------------------------------- ----------
72 xcms.retcor xset.RData rdata.xcms.retcor RData file 73 xcms.retcor xset.RData rdata.xcms.retcor RData file
73 ------------------------- ----------------- --------------------- ---------- 74 ------------------------- ----------------- -------------------------------- ----------
74 xcms.fillpeaks xset.RData rdata.xcms.fillpeaks RData file 75 xcms.fillpeaks xset.RData rdata.xcms.fillpeaks RData file
75 ------------------------- ----------------- --------------------- ---------- 76 ------------------------- ----------------- -------------------------------- ----------
76 CAMERA.annotate xset.RData rdata.camera.* RData file 77 CAMERA.annotate xset.RData rdata.camera.* RData file
77 ========================= ================= ===================== ========== 78 ========================= ================= ================================ ==========
78 79
79 80
80 .. image:: xcms_summary_workflow.png 81 .. image:: xcms_summary_workflow.png
81 82
82 --------------------------------------------------- 83 ---------------------------------------------------