Mercurial > repos > mmonsoor > camera_combinexsannos

comparison abims_CAMERA_combinexsAnnos.xml @ 8:198b035d4848 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419
author lecorguille
date Fri, 07 Apr 2017 07:42:38 -0400
parents 87570e9b71f5
children a3024f51082d
comparison
equal deleted inserted replaced
7:c23aa0cbc550 8:198b035d4848
1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.4"> 1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.6">
2 2
3 <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description> 3 <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description>
4 4
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 8
9 <expand macro="requirements"/> 9 <expand macro="requirements"/>
10 <expand macro="stdio"/> 10 <expand macro="stdio"/>
11 11
12 <command><![CDATA[ 12 <command><![CDATA[
13 @COMMAND_CAMERA_SCRIPT@ 13 @COMMAND_CAMERA_SCRIPT@
14 xfunction combinexsAnnos 14 xfunction combinexsAnnos
15 image_pos $image_pos 15 image_pos '$image_pos'
16 image_neg $image_neg 16 image_neg '$image_neg'
17 17
18 variableMetadataOutput $variableMetadata 18 variableMetadataOutput '$variableMetadata'
19 19
20 pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta 20 pos $pos tol $tol ruleset $ruleset keep_meta $keep_meta
21 21
22 convertRTMinute $export.convertRTMinute
23 numDigitsMZ $export.numDigitsMZ
24 numDigitsRT $export.numDigitsRT
25
22 ]]></command> 26 ]]></command>
23 27
24 <inputs> 28 <inputs>
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" /> 29 <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" />
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" /> 30 <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" />
27 31
28 <param name="pos" type="select" label="Returned peaklist polarity mode"> 32 <param name="pos" type="select" label="Returned peaklist polarity mode">
29 <option value="TRUE" selected="true">positive</option> 33 <option value="TRUE" selected="true">positive</option>
30 <option value="FALSE" >negative</option> 34 <option value="FALSE" >negative</option>
31 </param> 35 </param>
32 36
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" /> 37 <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" />
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!" /> 38 <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!" />
35 <param name="convert_param" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) rtmed, rtmin and rtmax into minutes"/>
36 <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/> 39 <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/>
37 40
41 <section name="export" title="Export options">
42 <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"/>
43 <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" />
44 <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" />
45 </section>
38 </inputs> 46 </inputs>
39 47
40 <outputs> 48 <outputs>
41 <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" /> 49 <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" />
42 <!-- 50 <!--
50 <param name="image_pos" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/> 58 <param name="image_pos" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/>
51 <param name="image_neg" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/> 59 <param name="image_neg" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/>
52 <param name="pos" value="TRUE"/> 60 <param name="pos" value="TRUE"/>
53 <param name="tol" value="2"/> 61 <param name="tol" value="2"/>
54 <param name="ruleset" value="1,1"/> 62 <param name="ruleset" value="1,1"/>
63 <section name="export">
64 <param name="convertRTMinute" value="True"/>
65 <param name="numDigitsMZ" value="4" />
66 <param name="numDigitsRT" value="1" />
67 </section>
55 <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" /> 68 <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
56 </test> 69 </test>
57 </tests> 70 </tests>
58 71
59 72
60 <help><![CDATA[ 73 <help><![CDATA[
61 74
62 @HELP_AUTHORS@ 75 @HELP_AUTHORS@
63 76
64 ======================= 77 =======================
65 Xcms.combinexsAnnos 78 Xcms.combinexsAnnos
66 ======================= 79 =======================
98 **Upstream tools** 111 **Upstream tools**
99 112
100 ========================= ======================= ===================== ========== 113 ========================= ======================= ===================== ==========
101 Name Output file Format Parameter 114 Name Output file Format Parameter
102 ========================= ======================= ===================== ========== 115 ========================= ======================= ===================== ==========
103 xcms.annotatediffreport xset.annotate_POS.RData rdata.camera.positive RData file 116 xcms.annotatediffreport xset.annotate_POS.RData rdata.camera.positive RData file
104 ------------------------- ----------------------- --------------------- ---------- 117 ------------------------- ----------------------- --------------------- ----------
105 xcms.annotatediffreport xset.annotate_NEG.RData rdata.camera.positive RData file 118 xcms.annotatediffreport xset.annotate_NEG.RData rdata.camera.positive RData file
106 ========================= ======================= ===================== ========== 119 ========================= ======================= ===================== ==========
107 120
108 **Downstream tools** 121 **Downstream tools**
109 122
110 +---------------------------+-----------------------------------------+--------+ 123 +---------------------------+-----------------------------------------+--------+
111 | Name | Output file | Format | 124 | Name | Output file | Format |
112 +===========================+=========================================+========+ 125 +===========================+=========================================+========+
125 | Batch_correction 138 | Batch_correction
126 | Filters 139 | Filters
127 | Univariate 140 | Univariate
128 | Multivariate PCA, PLS and OPLS 141 | Multivariate PCA, PLS and OPLS
129 142
143
144 **Place of CAMERA.combinexsannot after XCMS part of the metabolomic workflow**
145
146 .. image:: combinexsannos_workflow_zoom.png
130 147
131 **General schema of the metabolomic workflow** 148 **General schema of the metabolomic workflow**
132 149
133 .. image:: combinexsannos_workflow.png 150 .. image:: combinexsannos_workflow.png
134 151
151 168
152 xset.combinexsAnnos.variableMetadata.tsv 169 xset.combinexsAnnos.variableMetadata.tsv
153 170
154 | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results. 171 | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results.
155 | For each metabolite (row) : 172 | For each metabolite (row) :
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 173 | 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
157 174
158 xset.combinexsAnnos.Rdata 175 xset.combinexsAnnos.Rdata
159 176
160 | Rdata file, that be used outside Galaxy in R. 177 | Rdata file, that be used outside Galaxy in R.
161 178
162 179
163 --------------------------------------------------- 180 ---------------------------------------------------
164 181
165 --------------- 182 ---------------
166 Working example 183 Working example
190 --------------------------------------------------- 207 ---------------------------------------------------
191 208
192 Changelog/News 209 Changelog/News
193 -------------- 210 --------------
194 211
212 **Version 2.0.6 - 10/02/2017**
213
214 - IMPROVEMENT: Synchronize the variableMetadata export option with the other tools (xcms.group, xcms.fillpeaks, camera.annotate)
215
216
217 **Version 2.0.5 - 22/12/2016**
218
219 - IMPROVEMENT: add the possibility to add a personal Matrix of matching rules (ruleset)
220
195 **Version 2.0.4 - 21/04/2016** 221 **Version 2.0.4 - 21/04/2016**
196 222
197 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 223 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0
198 224
199 225
211 - IMPROVEMENT: parameter labels have changed to facilitate their reading. 237 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
212 238
213 239
214 **Version 2.0.0 - 09/06/2015** 240 **Version 2.0.0 - 09/06/2015**
215 241
216 - NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode 242 - NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode
217 243
218 244
219 ]]></help> 245 ]]></help>
220 246
221 <expand macro="citation" /> 247 <expand macro="citation" />
222 248
223 249
224 </tool> 250 </tool>
225
226