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annotate abims_CAMERA_combinexsAnnos.xml @ 9:a3024f51082d draft
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| author | lecorguille |
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| date | Wed, 29 Nov 2017 10:03:55 -0500 |
| parents | 198b035d4848 |
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1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.7"> |
| 0 | 2 |
| 3 <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description> | |
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4 |
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5 <macros> |
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6 <import>macros.xml</import> |
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7 </macros> |
| 0 | 8 |
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9 <expand macro="requirements"/> |
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10 <expand macro="stdio"/> |
| 0 | 11 |
| 3 | 12 <command><![CDATA[ |
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13 @COMMAND_CAMERA_SCRIPT@ |
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14 xfunction combinexsAnnos |
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15 image_pos '$image_pos' |
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16 image_neg '$image_neg' |
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18 variableMetadataOutput '$variableMetadata' |
| 3 | 19 |
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20 pos $pos tol $tol ruleset $ruleset keep_meta $keep_meta |
| 3 | 21 |
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22 convertRTMinute $export.convertRTMinute |
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23 numDigitsMZ $export.numDigitsMZ |
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24 numDigitsRT $export.numDigitsRT |
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25 |
| 3 | 26 ]]></command> |
| 0 | 27 |
| 28 <inputs> | |
| 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" /> | |
| 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" /> | |
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31 |
| 0 | 32 <param name="pos" type="select" label="Returned peaklist polarity mode"> |
| 33 <option value="TRUE" selected="true">positive</option> | |
| 34 <option value="FALSE" >negative</option> | |
| 35 </param> | |
| 36 | |
| 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" /> | |
| 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!" /> | |
| 39 <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/> | |
| 40 | |
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41 <section name="export" title="Export options"> |
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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"/> |
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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" /> |
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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" /> |
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45 </section> |
| 0 | 46 </inputs> |
| 47 | |
| 48 <outputs> | |
| 49 <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" /> | |
| 50 <!-- | |
| 51 <data name="rdata" format="rdata" label="${image_pos.name[:-6]}.combinexsAnnos.Rdata" /> | |
| 52 --> | |
| 53 </outputs> | |
| 54 | |
| 55 <tests> | |
| 56 <test> | |
| 57 <!-- TODO: generer des vrais dataset pos et neg--> | |
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58 <param name="image_pos" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/> |
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59 <param name="image_neg" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/> |
| 0 | 60 <param name="pos" value="TRUE"/> |
| 61 <param name="tol" value="2"/> | |
| 62 <param name="ruleset" value="1,1"/> | |
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63 <section name="export"> |
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64 <param name="convertRTMinute" value="True"/> |
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65 <param name="numDigitsMZ" value="4" /> |
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66 <param name="numDigitsRT" value="1" /> |
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67 </section> |
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68 <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" /> |
| 0 | 69 </test> |
| 70 </tests> | |
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71 |
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72 |
| 3 | 73 <help><![CDATA[ |
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75 @HELP_AUTHORS@ |
| 0 | 76 |
| 77 ======================= | |
| 78 Xcms.combinexsAnnos | |
| 79 ======================= | |
| 80 | |
| 81 ----------- | |
| 82 Description | |
| 83 ----------- | |
| 84 | |
| 85 **What it does?** | |
| 86 | |
| 87 This function check annotations of ion species with the help of a sample from opposite ion mode. | |
| 88 As first step it searches for pseudospectra from the positive and the negative sample within a reten- | |
| 89 tion time window. For every result the m/z differences between both samples are matched against | |
| 90 specific rules, which are combinations from pos. and neg. ion species. As example M+H and M-H | |
| 91 with a m/z difference of 2.014552. If two ions matches such a difference, the ion annotations are | |
| 92 changed (previous annotation is wrong), confirmed or added. Returns the peaklist from one ion | |
| 93 mode with recalculated annotations. | |
| 94 | |
| 95 **Details** | |
| 96 | |
| 97 Both xsAnnotate object should be full processed (grouping and annotation). Without previous anno- | |
| 98 tation the resulting peaklist only includes annotation with matches peaks from both mode according | |
| 99 to the rule(s). With ruleset=NULL the function only looks for M+H/M-H pairs. The ruleset is | |
| 100 a two column matrix with includes rule indices from the rule table of both xsAnnotate objects. | |
| 101 A ruleset (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and | |
| 102 xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined! | |
| 103 | |
| 104 | |
| 105 | |
| 106 ----------------- | |
| 107 Workflow position | |
| 108 ----------------- | |
| 109 | |
| 110 | |
| 111 **Upstream tools** | |
| 112 | |
| 113 ========================= ======================= ===================== ========== | |
| 114 Name Output file Format Parameter | |
| 115 ========================= ======================= ===================== ========== | |
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116 xcms.annotatediffreport xset.annotate_POS.RData rdata.camera.positive RData file |
| 0 | 117 ------------------------- ----------------------- --------------------- ---------- |
| 118 xcms.annotatediffreport xset.annotate_NEG.RData rdata.camera.positive RData file | |
| 119 ========================= ======================= ===================== ========== | |
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120 |
| 0 | 121 **Downstream tools** |
| 122 | |
| 123 +---------------------------+-----------------------------------------+--------+ | |
| 124 | Name | Output file | Format | | |
| 125 +===========================+=========================================+========+ | |
| 126 |Batch_correction |xset.combinexsAnnos.variableMetadata.tsv | Tabular| | |
| 127 +---------------------------+-----------------------------------------+--------+ | |
| 128 |Filters |xset.combinexsAnnos.variableMetadata.tsv | Tabular| | |
| 129 +---------------------------+-----------------------------------------+--------+ | |
| 130 |Univariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular| | |
| 131 +---------------------------+-----------------------------------------+--------+ | |
| 132 |Multivariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular| | |
| 133 +---------------------------+-----------------------------------------+--------+ | |
| 134 | |
| 135 | |
| 136 | |
| 137 The output file **xset.annotateDiffreport.variableMetadata.tsv** is a tabular file. You can continue your analysis using it in the following tools: | |
| 138 | Batch_correction | |
| 139 | Filters | |
| 140 | Univariate | |
| 141 | Multivariate PCA, PLS and OPLS | |
| 142 | |
| 143 | |
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144 **Place of CAMERA.combinexsannot after XCMS part of the metabolomic workflow** |
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145 |
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146 .. image:: combinexsannos_workflow_zoom.png |
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147 |
| 0 | 148 **General schema of the metabolomic workflow** |
| 149 | |
| 150 .. image:: combinexsannos_workflow.png | |
| 151 | |
| 152 | |
| 153 ----------- | |
| 154 Input files | |
| 155 ----------- | |
| 156 | |
| 157 +---------------------------+----------------------------+ | |
| 158 | Parameter : label | Format | | |
| 159 +===========================+============================+ | |
| 160 | Positive RData ion mode | rdata.camera.positive | | |
| 161 +---------------------------+----------------------------+ | |
| 162 | Negative RData ion mode | rdata.camera.negative | | |
| 163 +---------------------------+----------------------------+ | |
| 164 | |
| 165 ------------ | |
| 166 Output files | |
| 167 ------------ | |
| 168 | |
| 169 xset.combinexsAnnos.variableMetadata.tsv | |
| 170 | |
| 171 | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results. | |
| 172 | For each metabolite (row) : | |
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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 |
| 0 | 174 |
| 175 xset.combinexsAnnos.Rdata | |
| 176 | |
| 177 | Rdata file, that be used outside Galaxy in R. | |
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178 |
| 0 | 179 |
| 180 --------------------------------------------------- | |
| 181 | |
| 182 --------------- | |
| 183 Working example | |
| 184 --------------- | |
| 185 | |
| 186 Input files | |
| 187 ----------- | |
| 188 | |
| 189 | Positive RData ion mode -> **POS.xset.annotateDiffreport.RData** | |
| 190 | Negative RData ion mode -> **NEG.xset.annotateDiffreport.RData** | |
| 191 | |
| 192 Parameters | |
| 193 ---------- | |
| 194 | |
| 195 | pos -> **positive** | |
| 196 | tol -> **2 (default)** | |
| 197 | ruleset -> **1,1 (default)** | |
| 198 | |
| 199 Output files | |
| 200 ------------ | |
| 201 | |
| 202 **Example of an xset.combinexsAnnos.variableMetadata.tsv output:** | |
| 203 | |
| 204 .. image:: combinexsannos_variableMetadata.png | |
| 205 | |
| 3 | 206 |
| 207 --------------------------------------------------- | |
| 208 | |
| 209 Changelog/News | |
| 210 -------------- | |
| 211 | |
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212 **Version 2.0.7 - 29/11/2017** |
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213 |
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214 - BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C |
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215 |
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216 |
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217 **Version 2.0.6 - 10/02/2017** |
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218 |
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219 - IMPROVEMENT: Synchronize the variableMetadata export option with the other tools (xcms.group, xcms.fillpeaks, camera.annotate) |
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220 |
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221 |
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222 **Version 2.0.5 - 22/12/2016** |
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223 |
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224 - IMPROVEMENT: add the possibility to add a personal Matrix of matching rules (ruleset) |
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225 |
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226 **Version 2.0.4 - 21/04/2016** |
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227 |
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228 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 |
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229 |
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230 |
| 3 | 231 **Version 2.0.3 - 10/02/2016** |
| 232 | |
| 233 - BUGFIX: better management of errors. Datasets remained green although the process failed | |
| 234 | |
| 235 - UPDATE: refactoring of internal management of inputs/outputs | |
| 236 | |
| 237 | |
| 238 **Version 2.0.1 - 07/06/2015** | |
| 239 | |
| 240 - 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. | |
| 241 | |
| 242 - IMPROVEMENT: parameter labels have changed to facilitate their reading. | |
| 243 | |
| 244 | |
| 245 **Version 2.0.0 - 09/06/2015** | |
| 246 | |
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247 - NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode |
| 3 | 248 |
| 249 | |
| 250 ]]></help> | |
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planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
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