Mercurial > repos > lecorguille > xcms_fillpeaks

annotate abims_xcms_fillPeaks.xml @ 26:4db7afa8284d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 5583baab62c0f17cabbfe93ba4f2522e8df9b36b
author lecorguille
date Thu, 30 Mar 2017 08:35:34 -0400
parents 7e289788d37d
children 0544bc5967ed
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
22
a6938c381d4e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4
lecorguille
parents: 20
diff changeset
1 <tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.0">
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
2
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
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
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
4
6
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
5 <macros>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
6 <import>macros.xml</import>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
7 </macros>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
8
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
9 <expand macro="requirements"/>
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
10 <expand macro="stdio"/>
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
11
1
107a3de94c05 Uploaded
lecorguille
parents: 0
diff changeset
12 <command><![CDATA[
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
13 @COMMAND_XCMS_SCRIPT@
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
14 xfunction fillPeaks
22
a6938c381d4e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4
lecorguille
parents: 20
diff changeset
15 image '$image'
1
107a3de94c05 Uploaded
lecorguille
parents: 0
diff changeset
16
22
a6938c381d4e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4
lecorguille
parents: 20
diff changeset
17 xsetRdataOutput '$xsetRData'
1
107a3de94c05 Uploaded
lecorguille
parents: 0
diff changeset
18
107a3de94c05 Uploaded
lecorguille
parents: 0
diff changeset
19 method $method
107a3de94c05 Uploaded
lecorguille
parents: 0
diff changeset
20
20
02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 19
diff changeset
21 @COMMAND_PEAKLIST@
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
22
16
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
23 @COMMAND_FILE_LOAD@
10
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 9
diff changeset
24
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
25 @COMMAND_LOG_EXIT@
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
26
1
107a3de94c05 Uploaded
lecorguille
parents: 0
diff changeset
27 ]]></command>
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
28
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
29 <inputs>
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
30 <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another xcms function (group)" />
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
31 <param name="method" type="select" label="Filling method" help="[method] See the help section below">
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
32 <option value="chrom" selected="true">chrom</option>
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
33 <option value="MSW" >MSW</option>
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
34 </param>
20
02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 19
diff changeset
35
02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 19
diff changeset
36 <expand macro="input_peaklist"/>
02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 19
diff changeset
37
23
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 22
diff changeset
38 <expand macro="input_file_load"/>
10
35269602a971 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 960f403303e1691bdd6137c46895feb333b36a82
lecorguille
parents: 9
diff changeset
39
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
40 </inputs>
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
41
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
42 <outputs>
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
43 <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" />
20
02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 19
diff changeset
44 <expand macro="output_peaklist"/>
1
107a3de94c05 Uploaded
lecorguille
parents: 0
diff changeset
45 <data name="log" format="txt" label="xset.log.txt" hidden="true" />
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
46 </outputs>
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
47
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
48 <tests>
9
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
49 <!--<test>
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
50 <param name="image" value="xset.group.retcor.group.RData"/>
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
51 <param name="method" value="chrom"/>
6
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
52 <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" />
1
107a3de94c05 Uploaded
lecorguille
parents: 0
diff changeset
53 <output name="log">
107a3de94c05 Uploaded
lecorguille
parents: 0
diff changeset
54 <assert_contents>
6
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
55 <has_text text="object with 4 samples" />
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
56 <has_text text="Time range: 0.2-1140.1 seconds (0-19 minutes)" />
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
57 <has_text text="Mass range: 50.0021-999.9863 m/z" />
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
58 <has_text text="Peaks: 199718 (about 49930 per sample)" />
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
59 <has_text text="Peak Groups: 48958" />
1
107a3de94c05 Uploaded
lecorguille
parents: 0
diff changeset
60 <has_text text="Sample classes: bio, blank" />
107a3de94c05 Uploaded
lecorguille
parents: 0
diff changeset
61 </assert_contents>
107a3de94c05 Uploaded
lecorguille
parents: 0
diff changeset
62 </output>
9
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
63 </test>-->
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
64 <test>
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
65 <param name="image" value="faahKO.xset.group.retcor.group.RData"/>
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
66 <param name="method" value="chrom"/>
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
67 <conditional name="peaklist">
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
68 <param name="convertRTMinute" value="false" />
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
69 <param name="peaklistBool" value="true" />
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
70 <param name="numDigitsMZ" value="4" />
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
71 <param name="numDigitsRT" value="1" />
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
72 </conditional>
23
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 22
diff changeset
73 <expand macro="test_file_load_zip"/>
16
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
74 <output name="log">
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
75 <assert_contents>
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
76 <has_text text="object with 4 samples" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
77 <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
78 <has_text text="Mass range: 200.1-600 m/z" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
79 <has_text text="Peaks: 32720 (about 8180 per sample)" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
80 <has_text text="Peak Groups: 8157" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
81 <has_text text="Sample classes: KO, WT" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
82 </assert_contents>
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
83 </output>
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
84 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
85 <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
86 </test>
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
87 <test>
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
88 <param name="image" value="faahKO-single.xset.merged.group.retcor.group.RData"/>
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
89 <param name="method" value="chrom"/>
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
90 <conditional name="peaklist">
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
91 <param name="convertRTMinute" value="false" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
92 <param name="peaklistBool" value="true" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
93 <param name="numDigitsMZ" value="4" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
94 <param name="numDigitsRT" value="1" />
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
95 </conditional>
23
7e289788d37d planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 87dc789d7cd70a3733a1ad0b5a427f4d5905795d
lecorguille
parents: 22
diff changeset
96 <expand macro="test_file_load_single"/>
9
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
97 <output name="log">
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
98 <assert_contents>
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
99 <has_text text="object with 4 samples" />
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
100 <has_text text="Time range: 2506-4484 seconds (41.8-74.7 minutes)" />
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
101 <has_text text="Mass range: 200.1-600 m/z" />
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
102 <has_text text="Peaks: 32720 (about 8180 per sample)" />
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
103 <has_text text="Peak Groups: 8157" />
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
104 <has_text text="Sample classes: KO, WT" />
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
105 </assert_contents>
46f62282c8d8 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 727b4a74b8e424af622dc0e2b0c910cdd020cd29
lecorguille
parents: 6
diff changeset
106 </output>
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
107 <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.variableMetadata.tsv" />
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
108 <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
109 </test>
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
110 </tests>
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
111
1
107a3de94c05 Uploaded
lecorguille
parents: 0
diff changeset
112 <help><![CDATA[
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
113
6
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
114 @HELP_AUTHORS@
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
115
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
116 ==============
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
117 Xcms.fillPeaks
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
118 ==============
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
119
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
120 -----------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
121 Description
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
122 -----------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
123
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
124 **Integrate areas of missing peaks**
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
125 For each sample, identify peak groups where that sample is not
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
126 represented. For each of those peak groups, integrate the signal
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
127 in the region of that peak group and create a new peak.
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
128
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
129 According to the type of raw-data there are 2
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
130 different methods available. for filling gcms/lcms data the method
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
131 "chrom" integrates raw-data in the chromatographic domain, whereas
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
132 "MSW" is used for peaklists without retention-time information
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
133 like those from direct-infusion spectra.
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
134
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
135
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
136
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
137 -----------------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
138 Workflow position
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
139 -----------------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
140
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
141
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
142 **Upstream tools**
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
143
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
144 ========================= ================= ================== ==========
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
145 Name output file format parameter
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
146 ========================= ================= ================== ==========
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
147 xcms.group xset.group.RData rdata.xcms.group RData file
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
148 ========================= ================= ================== ==========
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
149
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
150
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
151 **Downstream tools**
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
152
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
153 +---------------------------+------------------+-----------------------+
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
154 | Name | Output file | Format |
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
155 +===========================+==================+=======================+
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
156 |CAMERA.annotate | xset.retcor.RData| rdata.xcms.fillpeaks |
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
157 +---------------------------+------------------+-----------------------+
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
158 |xcms.summary | xset.retcor.RData| rdata.xcms.fillpeaks |
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
159 +---------------------------+------------------+-----------------------+
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
160
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
161 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
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
162
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
163
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
164 **General schema of the metabolomic workflow**
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
165
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
166 .. image:: xcms_fillpeaks_workflow.png
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
167
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
168
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
169
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
170 -----------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
171 Input files
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
172 -----------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
173
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
174 +---------------------------+-----------------------+
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
175 | Parameter : num + label | Format |
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
176 +===========================+=======================+
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
177 | 1 : RData file | rdata.xcms.group |
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
178 +---------------------------+-----------------------+
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
179
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
180
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
181 ----------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
182 Parameters
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
183 ----------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
184
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
185
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
186 Method
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
187 ------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
188
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
189 **chrom**
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
190
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
191 | 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.
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
192 | 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).
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
193
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
194 **MSW**
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
195
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
196 | "MSW" is used for peaklists without retention-time information like those from direct-infusion spectra.
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
197
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
198
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
199 Get a Peak List
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
200 ---------------
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
201
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
202 If 'true', the module generates two additional files corresponding to the peak list:
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
203 - the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
204 - the data matrix (corresponding to related intensities)
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
205
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
206 **decimal places for [mass or retention time] values in identifiers**
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
207
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
208 | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
209 | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
210 | Theses parameters do not affect decimal places in columns other than the identifier one.
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
211
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
212 **Reported intensity values**
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
213
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
214 | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
215 | - into: integrated area of original (raw) peak
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
216 | - maxo: maximum intensity of original (raw) peak
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
217 | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
218
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
219 ------------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
220 Output files
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
221 ------------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
222
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
223 xset.fillPeaks.RData : rdata.xcms.fillpeaks format
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
224
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
225 | Rdata file that will be used in the **CAMERA.annotate** or **xcms.summary** step of the workflow.
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
226
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
227 xset.variableMetadata.tsv : tabular format
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
228
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
229 | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter* modules.
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
230
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
231 xset.dataMatrix.tsv : tabular format
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
232
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
233 | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter* modules.
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
234
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
235 ------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
236
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
237 .. class:: infomark
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
238
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
239 The output file is a xset.fillPeaks.RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool.
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
240
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
241
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
242 ---------------------------------------------------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
243
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
244 ---------------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
245 Working example
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
246 ---------------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
247
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
248 Input files
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
249 -----------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
250
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
251 | RData file -> **xset.retcor.RData**
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
252
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
253 Parameters
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
254 ----------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
255
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
256 | method -> **chrom**
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
257 | Get a Peak List -> **false**
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
258
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
259
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
260 Output files
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
261 ------------
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
262
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
263 | **xset.fillPeaks.RData: RData file**
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
264
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
265
5
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
266 ---------------------------------------------------
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
267
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
268 Changelog/News
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
269 --------------
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
270
22
a6938c381d4e planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b274c5c21db1a6ad63c28d425a7a6bce483a4af4
lecorguille
parents: 20
diff changeset
271 **Version 2.1.0 - 07/02/2017**
20
02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 19
diff changeset
272
02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 19
diff changeset
273 - IMPROVEMENT: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom)
02bb34af0921 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 481448087f0e09c131b24f7d552db69f3552d371-dirty
lecorguille
parents: 19
diff changeset
274
16
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
275 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data
5f61570177e2 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 22c4e92909198328fc7439ff47e4546a273eb907
lecorguille
parents: 15
diff changeset
276
15
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
277 **Version 2.0.8 - 22/12/2016**
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
278
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
279 - IMPROVEMENT: Add an option to export the peak list at this step without having to wait for CAMERA.annotate
1c78d61fd646 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 08e7f269a5c59687a7768be8db5fcb4e4d736093
lecorguille
parents: 12
diff changeset
280
12
1009f0279137 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 10
diff changeset
281 **Version 2.0.7 - 06/07/2016**
1009f0279137 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 10
diff changeset
282
1009f0279137 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 10
diff changeset
283 - UPGRADE: upgrate the xcms version from 1.44.0 to 1.46.0
1009f0279137 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit ec6f0c17bb277ea34f898d96d12d3357220f73d4
lecorguille
parents: 10
diff changeset
284
6
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
285 **Version 2.0.6 - 04/04/2016**
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
286
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
287 - TEST: refactoring to pass planemo test using conda dependencies
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
288
5
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
289 **Version 2.0.5 - 10/02/2016**
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
290
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
291 - BUGFIX: better management of errors. Datasets remained green although the process failed
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
292
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
293 - UPDATE: refactoring of internal management of inputs/outputs
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
294
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
295 - UPDATE: refactoring to feed the new report tool
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
296
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
297
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
298 **Version 2.0.2 - 02/06/2015**
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
299
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
300 - 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.
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
301
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
302 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
303
061958ded240 planemo upload
lecorguille
parents: 4
diff changeset
304
1
107a3de94c05 Uploaded
lecorguille
parents: 0
diff changeset
305 ]]></help>
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
306
6
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
307
f00e39a4b0fb planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents: 5
diff changeset
308 <expand macro="citation" />
0
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
309
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
310
30b01bcefda4 planemo upload
lecorguille
parents:
diff changeset
311 </tool>