annotate abims_CAMERA_combinexsAnnos.xml @ 6:ed26298f0246 draft

planemo upload commit f8a14a5bfd1843dc3f65b3f713c35dd62bf6996a-dirty
author lecorguille
date Mon, 04 Jul 2016 11:57:19 -0400
parents 87570e9b71f5
children 198b035d4848
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.4">
0
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
2
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
3 <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
4
4
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
5 <macros>
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
6 <import>macros.xml</import>
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
7 </macros>
0
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
8
4
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
9 <expand macro="requirements"/>
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
10 <expand macro="stdio"/>
0
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
11
3
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
12 <command><![CDATA[
4
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
13 @COMMAND_CAMERA_SCRIPT@
3
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
14 xfunction combinexsAnnos
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
15 image_pos $image_pos
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
16 image_neg $image_neg
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
17
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
18 variableMetadataOutput $variableMetadata
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
19
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
20 pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
21
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
22 ]]></command>
0
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
23
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
24 <inputs>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
25 <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" />
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
26 <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" />
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
27
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
28 <param name="pos" type="select" label="Returned peaklist polarity mode">
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
29 <option value="TRUE" selected="true">positive</option>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
30 <option value="FALSE" >negative</option>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
31 </param>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
32
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
33 <param name="tol" type="integer" value="2" label="Retention time window in seconds" help="[pos] As first step it searches for pseudospectra from the positive and the negative sample within a retention time window" />
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
34 <param name="ruleset" type="text" value="1,1" label="Matrix of matching rules" help="[ruleset] Matrix of matching rules. By default, the matrix (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!" />
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
35 <param name="convert_param" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) rtmed, rtmin and rtmax into minutes"/>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
36 <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
37
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
38 </inputs>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
39
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
40 <outputs>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
41 <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" />
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
42 <!--
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
43 <data name="rdata" format="rdata" label="${image_pos.name[:-6]}.combinexsAnnos.Rdata" />
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
44 -->
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
45 </outputs>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
46
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
47 <tests>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
48 <test>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
49 <!-- TODO: generer des vrais dataset pos et neg-->
4
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
50 <param name="image_pos" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/>
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
51 <param name="image_neg" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/>
0
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
52 <param name="pos" value="TRUE"/>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
53 <param name="tol" value="2"/>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
54 <param name="ruleset" value="1,1"/>
4
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
55 <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
0
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
56 </test>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
57 </tests>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
58
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
59
3
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
60 <help><![CDATA[
4
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
61
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
62 @HELP_AUTHORS@
0
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
63
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
64 =======================
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
65 Xcms.combinexsAnnos
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
66 =======================
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
67
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
68 -----------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
69 Description
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
70 -----------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
71
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
72 **What it does?**
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
73
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
74 This function check annotations of ion species with the help of a sample from opposite ion mode.
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
75 As first step it searches for pseudospectra from the positive and the negative sample within a reten-
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
76 tion time window. For every result the m/z differences between both samples are matched against
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
77 specific rules, which are combinations from pos. and neg. ion species. As example M+H and M-H
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
78 with a m/z difference of 2.014552. If two ions matches such a difference, the ion annotations are
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
79 changed (previous annotation is wrong), confirmed or added. Returns the peaklist from one ion
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
80 mode with recalculated annotations.
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
81
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
82 **Details**
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
83
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
84 Both xsAnnotate object should be full processed (grouping and annotation). Without previous anno-
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
85 tation the resulting peaklist only includes annotation with matches peaks from both mode according
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
86 to the rule(s). With ruleset=NULL the function only looks for M+H/M-H pairs. The ruleset is
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
87 a two column matrix with includes rule indices from the rule table of both xsAnnotate objects.
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
88 A ruleset (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
89 xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
90
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
91
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
92
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
93 -----------------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
94 Workflow position
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
95 -----------------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
96
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
97
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
98 **Upstream tools**
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
99
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
100 ========================= ======================= ===================== ==========
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
101 Name Output file Format Parameter
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
102 ========================= ======================= ===================== ==========
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
103 xcms.annotatediffreport xset.annotate_POS.RData rdata.camera.positive RData file
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
104 ------------------------- ----------------------- --------------------- ----------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
105 xcms.annotatediffreport xset.annotate_NEG.RData rdata.camera.positive RData file
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
106 ========================= ======================= ===================== ==========
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
107
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
108 **Downstream tools**
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
109
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
110 +---------------------------+-----------------------------------------+--------+
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
111 | Name | Output file | Format |
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
112 +===========================+=========================================+========+
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
113 |Batch_correction |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
114 +---------------------------+-----------------------------------------+--------+
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
115 |Filters |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
116 +---------------------------+-----------------------------------------+--------+
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
117 |Univariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
118 +---------------------------+-----------------------------------------+--------+
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
119 |Multivariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular|
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
120 +---------------------------+-----------------------------------------+--------+
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
121
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
122
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
123
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
124 The output file **xset.annotateDiffreport.variableMetadata.tsv** is a tabular file. You can continue your analysis using it in the following tools:
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
125 | Batch_correction
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
126 | Filters
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
127 | Univariate
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
128 | Multivariate PCA, PLS and OPLS
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
129
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
130
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
131 **General schema of the metabolomic workflow**
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
132
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
133 .. image:: combinexsannos_workflow.png
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
134
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
135
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
136 -----------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
137 Input files
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
138 -----------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
139
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
140 +---------------------------+----------------------------+
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
141 | Parameter : label | Format |
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
142 +===========================+============================+
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
143 | Positive RData ion mode | rdata.camera.positive |
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
144 +---------------------------+----------------------------+
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
145 | Negative RData ion mode | rdata.camera.negative |
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
146 +---------------------------+----------------------------+
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
147
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
148 ------------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
149 Output files
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
150 ------------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
151
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
152 xset.combinexsAnnos.variableMetadata.tsv
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
153
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
154 | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results.
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
155 | For each metabolite (row) :
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
156 | the value of the intensity in each sample, fold, tstat, pvalue, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct, pcgroup and neg (or pos). Mode
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
157
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
158 xset.combinexsAnnos.Rdata
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
159
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
160 | Rdata file, that be used outside Galaxy in R.
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
161
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
162
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
163 ---------------------------------------------------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
164
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
165 ---------------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
166 Working example
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
167 ---------------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
168
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
169 Input files
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
170 -----------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
171
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
172 | Positive RData ion mode -> **POS.xset.annotateDiffreport.RData**
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
173 | Negative RData ion mode -> **NEG.xset.annotateDiffreport.RData**
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
174
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
175 Parameters
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
176 ----------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
177
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
178 | pos -> **positive**
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
179 | tol -> **2 (default)**
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
180 | ruleset -> **1,1 (default)**
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
181
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
182 Output files
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
183 ------------
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
184
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
185 **Example of an xset.combinexsAnnos.variableMetadata.tsv output:**
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
186
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
187 .. image:: combinexsannos_variableMetadata.png
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
188
3
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
189
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
190 ---------------------------------------------------
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
191
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
192 Changelog/News
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
193 --------------
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
194
4
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
195 **Version 2.0.4 - 21/04/2016**
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
196
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
197 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
198
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
199
3
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
200 **Version 2.0.3 - 10/02/2016**
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
201
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
202 - BUGFIX: better management of errors. Datasets remained green although the process failed
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
203
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
204 - UPDATE: refactoring of internal management of inputs/outputs
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
205
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
206
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
207 **Version 2.0.1 - 07/06/2015**
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
208
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
209 - IMPROVEMENT: new datatype/dataset formats (rdata.camera.positive, rdata.camera.negative, rdata.camera.quick ...) will facilitate the sequence of tools and so avoid incompatibility errors.
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
210
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
211 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
212
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
213
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
214 **Version 2.0.0 - 09/06/2015**
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
215
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
216 - NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
217
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
218
4ca5c7bbc6cf planemo upload
lecorguille
parents: 0
diff changeset
219 ]]></help>
0
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
220
4
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents: 3
diff changeset
221 <expand macro="citation" />
0
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
222
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
223
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
224 </tool>
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
225
0c730c636867 planemo upload
mmonsoor
parents:
diff changeset
226