Mercurial > repos > lecorguille > xcms_summary
annotate abims_xcms_summary.xml @ 19:0cc47a5ebca9 draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 37b0a6a7686f701e4bf00db97ae2c1b82cd6e989
author | lecorguille |
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date | Fri, 09 Nov 2018 15:19:29 -0500 |
parents | 97ca0321931b |
children | 46be2c523a7f |
rev | line source |
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97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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1 <tool id="abims_xcms_summary" name="xcms process history" version="@WRAPPER_VERSION@.0"> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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2 |
0 | 3 <description>Create a summary of XCMS analysis</description> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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4 |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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5 <macros> |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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6 <import>macros.xml</import> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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7 <import>macros_xcms.xml</import> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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8 </macros> |
6
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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9 |
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97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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10 <expand macro="requirements"> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
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11 <requirement type="package" version="1.32.0">bioconductor-camera</requirement> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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12 </expand> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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13 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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14 <expand macro="stdio"/> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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15 |
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ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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16 <command><![CDATA[ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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17 @COMMAND_RSCRIPT@/xcms_summary.r |
0 | 18 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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19 image '$image' |
27e7da5f6848
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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20 htmlOutput '$htmlOutput' |
0 | 21 user_email $__user_email__ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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22 |
0 | 23 ]]></command> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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24 |
0 | 25 <inputs> |
26 | |
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97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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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.)" /> |
0 | 28 |
29 </inputs> | |
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27e7da5f6848
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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30 |
0 | 31 <outputs> |
32 <data name="htmlOutput" format="html" label="xcms summary html" /> | |
33 </outputs> | |
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27e7da5f6848
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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34 |
0 | 35 <tests> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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36 <!--<test> |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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37 <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData" ftype="rdata"/> |
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27e7da5f6848
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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38 <output name="htmlOutput" file="faahKO.xset.group.retcor.group.fillpeaks.summary.html" /> |
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97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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39 </test>--> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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40 <test> |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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41 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData" ftype="rdata"/> |
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27e7da5f6848
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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42 <output name="htmlOutput" file="faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html" /> |
0 | 43 </test> |
44 </tests> | |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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45 |
0 | 46 <help><![CDATA[ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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47 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
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48 @HELP_AUTHORS@ |
0 | 49 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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50 ==================== |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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51 xcms process history |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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52 ==================== |
0 | 53 |
54 ----------- | |
55 Description | |
56 ----------- | |
57 | |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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58 This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools |
27e7da5f6848
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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59 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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60 ----------------- |
27e7da5f6848
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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61 Workflow position |
27e7da5f6848
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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62 ----------------- |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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63 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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64 **Upstream tools** |
0 | 65 |
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66 ========================= =========================== ================================ |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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67 Name Output file Format |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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68 ========================= =========================== ================================ |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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69 xcms.findChromPeaks xset.RData rdata.xcms.findchrompeaks |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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70 ------------------------- --------------------------- -------------------------------- |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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71 xcms.groupChromPeaks ``*``.groupChromPeaks.RData rdata.xcms.group |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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72 ------------------------- --------------------------- -------------------------------- |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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73 xcms.adjustRtime ``*``.adjustRtime.RData rdata.xcms.retcor |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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74 ------------------------- --------------------------- -------------------------------- |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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75 xcms.fillChromPeaks ``*``.fillChromPeaks.RData rdata.xcms.fillpeaks |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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76 ------------------------- --------------------------- -------------------------------- |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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77 CAMERA.annotate ``*``.annotate.*.RData rdata.camera.``*`` |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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78 ========================= =========================== ================================ |
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79 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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80 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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81 .. image:: xcms_summary_workflow.png |
0 | 82 |
83 --------------------------------------------------- | |
84 | |
85 Changelog/News | |
86 -------------- | |
87 | |
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88 **Version 3.0.0.0 - 14/02/2018** |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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89 |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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90 - UPGRADE: upgrade the xcms version from 1.46.0 to 3.0.0. So refactoring of a lot of underlying codes and methods |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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91 |
97ca0321931b
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92 - IMPROVEMENT: the tool now shows all the parameters and not only those which were set. |
97ca0321931b
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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93 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 9f72e947d9c241d11221cad561f3525d27231857
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94 |
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95 **Version 1.0.4 - 13/02/2018** |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
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96 |
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97 - UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0 |
4c757d1ba7b4
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298
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98 |
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99 |
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100 **Version 1.0.3 - 03/02/2017** |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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101 |
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102 - IMPROVEMENT: xcms.summary can deal with merged individual data |
27e7da5f6848
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit a6f5f18b3d6130f7d7fbb9f2df856838c6217797
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103 |
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104 |
10
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105 **Version 1.0.2 - 06/07/2016** |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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106 |
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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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107 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0 |
420f42a57916
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
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108 |
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109 |
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ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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110 **Version 1.0.1 - 04/04/2016** |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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111 |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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112 - TEST: refactoring to pass planemo test using conda dependencies |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents:
5
diff
changeset
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113 |
ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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114 |
0 | 115 **Version 1.0.0 - 10/02/2016** |
116 | |
117 - NEW: Create a summary of XCMS analysis | |
118 | |
119 | |
120 ]]></help> | |
121 | |
122 | |
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ca7c9a6da2c6
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
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123 <expand macro="citation" /> |
0 | 124 |
125 </tool> |