annotate abims_xcms_fillPeaks.xml @ 10:6caa60dcc217 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 30bf079aba283d5b37a77cbd8996592ad99eca8c
author lecorguille
date Tue, 07 Feb 2017 04:05:02 -0500
parents ee29f0a6e361
children de0d85537ee3
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.8">
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
2
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
3 <description>Integrate a sample's signal in regions where peak groups are not represented to create new peaks in missing areas</description>
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
4
4
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
5 <macros>
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
6 <import>macros.xml</import>
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
7 </macros>
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
8
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
9 <expand macro="requirements"/>
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
10 <expand macro="stdio"/>
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
11
3
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
12 <command><![CDATA[
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
13 @COMMAND_XCMS_SCRIPT@
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
14 xfunction fillPeaks
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
15 image $image
3
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
16
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
17 xsetRdataOutput $xsetRData
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
18
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
19 method $method
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
20
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
21 #if $peaklist.peaklistBool
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
22 variableMetadataOutput $variableMetadata
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
23 dataMatrixOutput $dataMatrix
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
24 convertRTMinute $peaklist.convertRTMinute
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
25 numDigitsMZ $peaklist.numDigitsMZ
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
26 numDigitsRT $peaklist.numDigitsRT
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
27 intval $peaklist.intval
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
28 #end if
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
29
6
465623d2f6fa planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 5
diff changeset
30 @COMMAND_ZIPFILE_LOAD@
465623d2f6fa planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 5
diff changeset
31
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
32 @COMMAND_LOG_EXIT@
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
33
3
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
34 ]]></command>
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
35
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
36 <inputs>
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
37 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" />
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
38 <param name="method" type="select" label="Filling method" help="[method] See the help section below">
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
39 <option value="chrom" selected="true">chrom</option>
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
40 <option value="MSW" >MSW</option>
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
41 </param>
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
42 <conditional name="peaklist">
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
43 <param name="peaklistBool" type="boolean" label="Get a Peak List" />
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
44 <when value="true">
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
45 <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
46 <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
47 <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
48 <param name="intval" type="select" label="Reported intensity values" help="[intval] See the help section below">
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
49 <option value="into" selected="true">into</option>
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
50 <option value="maxo">maxo</option>
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
51 <option value="intb">intb</option>
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
52 </param>
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
53 </when>
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
54 <when value="false" />
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
55 </conditional>
6
465623d2f6fa planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 5
diff changeset
56 <expand macro="zipfile_load"/>
465623d2f6fa planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 5
diff changeset
57
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
58 </inputs>
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
59
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
60 <outputs>
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
61 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" />
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
62 <data name="variableMetadata" format="tabular" label="${image.name[:-6]}.fillPeaks.variableMetadata.tsv">
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
63 <filter>(peaklist['peaklistBool'])</filter>
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
64 </data>
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
65 <data name="dataMatrix" format="tabular" label="${image.name[:-6]}.fillPeaks.dataMatrix.tsv" >
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
66 <filter>(peaklist['peaklistBool'])</filter>
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
67 </data>
3
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
68 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
69 </outputs>
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
70
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
71 <tests>
5
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
72 <!--<test>
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
73 <param name="image" value="xset.group.retcor.group.RData"/>
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
74 <param name="method" value="chrom"/>
4
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
75 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" />
3
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
76 <output name="log">
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
77 <assert_contents>
4
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
78 <has_text text="object with 4 samples" />
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
79 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
80 <has_text text="Mass range: 50.0021-999.9863 m/z" />
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
81 <has_text text="Peaks: 199718 (about 49930 per sample)" />
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
82 <has_text text="Peak Groups: 48958" />
3
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
83 <has_text text="Sample classes: bio, blank" />
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
84 </assert_contents>
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
85 </output>
5
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
86 </test>-->
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
87 <test>
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
88 <param name="image" value="faahKO.xset.group.retcor.group.RData"/>
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
89 <param name="method" value="chrom"/>
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
90 <conditional name="peaklist">
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
91 <param name="convertRTMinute" value="false" />
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
92 <param name="peaklistBool" value="true" />
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
93 <param name="numDigitsMZ" value="4" />
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
94 <param name="numDigitsRT" value="1" />
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
95 </conditional>
6
465623d2f6fa planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 5
diff changeset
96 <param name="zipfile_load_conditional|zipfile_load_select" value="yes" />
465623d2f6fa planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 5
diff changeset
97 <param name="zipfile_load_conditional|zip_file" value="faahKO_reduce.zip" ftype="zip" />
5
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
98 <output name="log">
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
99 <assert_contents>
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
100 <has_text text="object with 4 samples" />
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
101 <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" />
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
102 <has_text text="Mass range: 200.1-600 m/z" />
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
103 <has_text text="Peaks: 32720 (about 8180 per sample)" />
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
104 <has_text text="Peak Groups: 8157" />
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
105 <has_text text="Sample classes: KO, WT" />
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
106 </assert_contents>
cd351af95d14 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 4
diff changeset
107 </output>
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
108 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
109 <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
110 </test>
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
111 </tests>
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
112
3
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
113 <help><![CDATA[
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
114
4
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
115 @HELP_AUTHORS@
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
116
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
117 ==============
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
118 Xcms.fillPeaks
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
119 ==============
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
120
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
121 -----------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
122 Description
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
123 -----------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
124
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
125 **Integrate areas of missing peaks**
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
126 For each sample, identify peak groups where that sample is not
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
127 represented. For each of those peak groups, integrate the signal
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
128 in the region of that peak group and create a new peak.
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
129
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
130 According to the type of raw-data there are 2
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
131 different methods available. for filling gcms/lcms data the method
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
132 "chrom" integrates raw-data in the chromatographic domain, whereas
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
133 "MSW" is used for peaklists without retention-time information
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
134 like those from direct-infusion spectra.
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
135
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
136
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
137
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
138 -----------------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
139 Workflow position
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
140 -----------------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
141
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
142
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
143 **Upstream tools**
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
144
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
145 ========================= ================= ================== ==========
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
146 Name output file format parameter
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
147 ========================= ================= ================== ==========
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
148 xcms.group xset.group.RData rdata.xcms.group RData file
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
149 ========================= ================= ================== ==========
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
150
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
151
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
152 **Downstream tools**
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
153
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
154 +---------------------------+------------------+-----------------------+
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
155 | Name | Output file | Format |
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
156 +===========================+==================+=======================+
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
157 |CAMERA.annotate | xset.retcor.RData| rdata.xcms.fillpeaks |
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
158 +---------------------------+------------------+-----------------------+
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
159 |xcms.summary | xset.retcor.RData| rdata.xcms.fillpeaks |
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
160 +---------------------------+------------------+-----------------------+
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
161
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
162 The output file **xset.fillpeaks** is a RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool as a following step of your workflow.
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
163
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
164
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
165 **General schema of the metabolomic workflow**
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
166
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
167 .. image:: xcms_fillpeaks_workflow.png
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
168
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
169
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
170
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
171 -----------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
172 Input files
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
173 -----------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
174
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
175 +---------------------------+-----------------------+
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
176 | Parameter : num + label | Format |
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
177 +===========================+=======================+
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
178 | 1 : RData file | rdata.xcms.group |
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
179 +---------------------------+-----------------------+
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
180
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
181
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
182 ----------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
183 Parameters
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
184 ----------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
185
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
186
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
187 Method
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
188 ------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
189
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
190 **chrom**
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
191
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
192 | This method produces intensity values for those missing samples by integrating raw data in peak group region. In a given group, the start and ending retention time points for integration are defined by the median start and end points of the other detected peaks. The start and end m/z values are similarly determined. Intensities can be still be zero, which is a rather unusual intensity for a peak. This is the case if e.g. the raw data was threshholded, and the integration area contains no actual raw intensities, or if one sample is miscalibrated, such the raw data points are (just) outside the integration area.
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
193 | Importantly, if retention time correction data is available, the alignment information is used to more precisely integrate the propper region of the raw data. If the corrected retention time is beyond the end of the raw data, the value will be not-a-number (NaN).
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
194
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
195 **MSW**
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
196
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
197 | "MSW" is used for peaklists without retention-time information like those from direct-infusion spectra.
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
198
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
199
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
200 Get a Peak List
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
201 ---------------
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
202
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
203 If 'true', the module generates two additional files corresponding to the peak list:
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
204 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
205 - the data matrix (corresponding to related intensities)
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
206
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
207 **decimal places for [mass or retention time] values in identifiers**
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
208
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
209 | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
210 | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
211 | Theses parameters do not affect decimal places in columns other than the identifier one.
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
212
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
213 **Reported intensity values**
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
214
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
215 | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
216 | - into: integrated area of original (raw) peak
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
217 | - maxo: maximum intensity of original (raw) peak
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
218 | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
219
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
220 ------------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
221 Output files
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
222 ------------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
223
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
224 xset.fillPeaks.RData : rdata.xcms.fillpeaks format
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
225
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
226 | Rdata file that will be used in the **CAMERA.annotate** or **xcms.summary** step of the workflow.
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
227
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
228 xset.variableMetadata.tsv : tabular format
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
229
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
230 | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter* modules.
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
231
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
232 xset.dataMatrix.tsv : tabular format
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
233
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
234 | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter* modules.
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
235
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
236 ------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
237
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
238 .. class:: infomark
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
239
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
240 The output file is a xset.fillPeaks.RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool.
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
241
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
242
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
243 ---------------------------------------------------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
244
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
245 ---------------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
246 Working example
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
247 ---------------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
248
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
249 Input files
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
250 -----------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
251
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
252 | RData file -> **xset.retcor.RData**
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
253
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
254 Parameters
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
255 ----------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
256
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
257 | method -> **chrom**
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
258 | Get a Peak List -> **false**
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
259
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
260
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
261 Output files
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
262 ------------
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
263
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
264 | **xset.fillPeaks.RData: RData file**
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
265
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
266
3
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
267 ---------------------------------------------------
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
268
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
269 Changelog/News
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
270 --------------
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
271
9
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
272 **Version 2.0.8 - 22/12/2016**
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
273
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
274 - IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate
ee29f0a6e361 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 8
diff changeset
275
8
cce30b3398e0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 6
diff changeset
276 **Version 2.0.7 - 06/07/2016**
cce30b3398e0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 6
diff changeset
277
cce30b3398e0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 6
diff changeset
278 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
cce30b3398e0 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 6
diff changeset
279
4
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
280 **Version 2.0.6 - 04/04/2016**
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
281
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
282 - TEST: refactoring to pass planemo test using conda dependencies
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
283
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
284
3
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
285 **Version 2.0.5 - 10/02/2016**
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
286
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
287 - BUGFIX: better management of errors. Datasets remained green although the process failed
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
288
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
289 - UPDATE: refactoring of internal management of inputs/outputs
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
290
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
291 - UPDATE: refactoring to feed the new report tool
2
5815e6e11f9b Uploaded
mmonsoor
parents: 0
diff changeset
292
5815e6e11f9b Uploaded
mmonsoor
parents: 0
diff changeset
293
3
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
294 **Version 2.0.2 - 02/06/2015**
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
295
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
296 - IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
297
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
298 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
299
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
300
5a54397dbc97 planemo upload
lecorguille
parents: 2
diff changeset
301 ]]></help>
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
302
4
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
303
2edfa5e1f719 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
lecorguille
parents: 3
diff changeset
304 <expand macro="citation" />
0
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
305
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
306
022df2ef15b0 planemo upload
lecorguille
parents:
diff changeset
307 </tool>