Mercurial > repos > mmonsoor > camera_combinexsannos
annotate abims_CAMERA_combinexsAnnos.xml @ 6:ed26298f0246 draft
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| author | lecorguille |
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| date | Mon, 04 Jul 2016 11:57:19 -0400 |
| parents | 87570e9b71f5 |
| children | 198b035d4848 |
| rev | line source |
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1 <tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.4"> |
| 0 | 2 |
| 3 <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description> | |
| 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@ |
| 3 | 14 xfunction combinexsAnnos |
| 15 image_pos $image_pos | |
| 16 image_neg $image_neg | |
| 17 | |
| 18 variableMetadataOutput $variableMetadata | |
| 19 | |
| 20 pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta | |
| 21 | |
| 22 ]]></command> | |
| 0 | 23 |
| 24 <inputs> | |
| 25 <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" /> | |
| 26 <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" /> | |
| 27 | |
| 28 <param name="pos" type="select" label="Returned peaklist polarity mode"> | |
| 29 <option value="TRUE" selected="true">positive</option> | |
| 30 <option value="FALSE" >negative</option> | |
| 31 </param> | |
| 32 | |
| 33 <param name="tol" type="integer" value="2" label="Retention time window in seconds" help="[pos] As first step it searches for pseudospectra from the positive and the negative sample within a retention time window" /> | |
| 34 <param name="ruleset" type="text" value="1,1" label="Matrix of matching rules" help="[ruleset] Matrix of matching rules. By default, the matrix (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!" /> | |
| 35 <param name="convert_param" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) rtmed, rtmin and rtmax into minutes"/> | |
| 36 <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/> | |
| 37 | |
| 38 </inputs> | |
| 39 | |
| 40 <outputs> | |
| 41 <data name="variableMetadata" format="tabular" label="${image_pos.name[:-6]}.combinexsAnnos.variableMetadata.tsv" /> | |
| 42 <!-- | |
| 43 <data name="rdata" format="rdata" label="${image_pos.name[:-6]}.combinexsAnnos.Rdata" /> | |
| 44 --> | |
| 45 </outputs> | |
| 46 | |
| 47 <tests> | |
| 48 <test> | |
| 49 <!-- TODO: generer des vrais dataset pos et neg--> | |
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50 <param name="image_pos" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.Rdata"/> |
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51 <param name="image_neg" value="faahOK.xset.group.retcor.group.fillPeaks.annotate.negative.Rdata"/> |
| 0 | 52 <param name="pos" value="TRUE"/> |
| 53 <param name="tol" value="2"/> | |
| 54 <param name="ruleset" value="1,1"/> | |
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55 <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" /> |
| 0 | 56 </test> |
| 57 </tests> | |
| 58 | |
| 59 | |
| 3 | 60 <help><![CDATA[ |
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61 |
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62 @HELP_AUTHORS@ |
| 0 | 63 |
| 64 ======================= | |
| 65 Xcms.combinexsAnnos | |
| 66 ======================= | |
| 67 | |
| 68 ----------- | |
| 69 Description | |
| 70 ----------- | |
| 71 | |
| 72 **What it does?** | |
| 73 | |
| 74 This function check annotations of ion species with the help of a sample from opposite ion mode. | |
| 75 As first step it searches for pseudospectra from the positive and the negative sample within a reten- | |
| 76 tion time window. For every result the m/z differences between both samples are matched against | |
| 77 specific rules, which are combinations from pos. and neg. ion species. As example M+H and M-H | |
| 78 with a m/z difference of 2.014552. If two ions matches such a difference, the ion annotations are | |
| 79 changed (previous annotation is wrong), confirmed or added. Returns the peaklist from one ion | |
| 80 mode with recalculated annotations. | |
| 81 | |
| 82 **Details** | |
| 83 | |
| 84 Both xsAnnotate object should be full processed (grouping and annotation). Without previous anno- | |
| 85 tation the resulting peaklist only includes annotation with matches peaks from both mode according | |
| 86 to the rule(s). With ruleset=NULL the function only looks for M+H/M-H pairs. The ruleset is | |
| 87 a two column matrix with includes rule indices from the rule table of both xsAnnotate objects. | |
| 88 A ruleset (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and | |
| 89 xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined! | |
| 90 | |
| 91 | |
| 92 | |
| 93 ----------------- | |
| 94 Workflow position | |
| 95 ----------------- | |
| 96 | |
| 97 | |
| 98 **Upstream tools** | |
| 99 | |
| 100 ========================= ======================= ===================== ========== | |
| 101 Name Output file Format Parameter | |
| 102 ========================= ======================= ===================== ========== | |
| 103 xcms.annotatediffreport xset.annotate_POS.RData rdata.camera.positive RData file | |
| 104 ------------------------- ----------------------- --------------------- ---------- | |
| 105 xcms.annotatediffreport xset.annotate_NEG.RData rdata.camera.positive RData file | |
| 106 ========================= ======================= ===================== ========== | |
| 107 | |
| 108 **Downstream tools** | |
| 109 | |
| 110 +---------------------------+-----------------------------------------+--------+ | |
| 111 | Name | Output file | Format | | |
| 112 +===========================+=========================================+========+ | |
| 113 |Batch_correction |xset.combinexsAnnos.variableMetadata.tsv | Tabular| | |
| 114 +---------------------------+-----------------------------------------+--------+ | |
| 115 |Filters |xset.combinexsAnnos.variableMetadata.tsv | Tabular| | |
| 116 +---------------------------+-----------------------------------------+--------+ | |
| 117 |Univariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular| | |
| 118 +---------------------------+-----------------------------------------+--------+ | |
| 119 |Multivariate |xset.combinexsAnnos.variableMetadata.tsv | Tabular| | |
| 120 +---------------------------+-----------------------------------------+--------+ | |
| 121 | |
| 122 | |
| 123 | |
| 124 The output file **xset.annotateDiffreport.variableMetadata.tsv** is a tabular file. You can continue your analysis using it in the following tools: | |
| 125 | Batch_correction | |
| 126 | Filters | |
| 127 | Univariate | |
| 128 | Multivariate PCA, PLS and OPLS | |
| 129 | |
| 130 | |
| 131 **General schema of the metabolomic workflow** | |
| 132 | |
| 133 .. image:: combinexsannos_workflow.png | |
| 134 | |
| 135 | |
| 136 ----------- | |
| 137 Input files | |
| 138 ----------- | |
| 139 | |
| 140 +---------------------------+----------------------------+ | |
| 141 | Parameter : label | Format | | |
| 142 +===========================+============================+ | |
| 143 | Positive RData ion mode | rdata.camera.positive | | |
| 144 +---------------------------+----------------------------+ | |
| 145 | Negative RData ion mode | rdata.camera.negative | | |
| 146 +---------------------------+----------------------------+ | |
| 147 | |
| 148 ------------ | |
| 149 Output files | |
| 150 ------------ | |
| 151 | |
| 152 xset.combinexsAnnos.variableMetadata.tsv | |
| 153 | |
| 154 | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results. | |
| 155 | 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 | |
| 157 | |
| 158 xset.combinexsAnnos.Rdata | |
| 159 | |
| 160 | Rdata file, that be used outside Galaxy in R. | |
| 161 | |
| 162 | |
| 163 --------------------------------------------------- | |
| 164 | |
| 165 --------------- | |
| 166 Working example | |
| 167 --------------- | |
| 168 | |
| 169 Input files | |
| 170 ----------- | |
| 171 | |
| 172 | Positive RData ion mode -> **POS.xset.annotateDiffreport.RData** | |
| 173 | Negative RData ion mode -> **NEG.xset.annotateDiffreport.RData** | |
| 174 | |
| 175 Parameters | |
| 176 ---------- | |
| 177 | |
| 178 | pos -> **positive** | |
| 179 | tol -> **2 (default)** | |
| 180 | ruleset -> **1,1 (default)** | |
| 181 | |
| 182 Output files | |
| 183 ------------ | |
| 184 | |
| 185 **Example of an xset.combinexsAnnos.variableMetadata.tsv output:** | |
| 186 | |
| 187 .. image:: combinexsannos_variableMetadata.png | |
| 188 | |
| 3 | 189 |
| 190 --------------------------------------------------- | |
| 191 | |
| 192 Changelog/News | |
| 193 -------------- | |
| 194 | |
|
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195 **Version 2.0.4 - 21/04/2016** |
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196 |
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197 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 |
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198 |
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199 |
| 3 | 200 **Version 2.0.3 - 10/02/2016** |
| 201 | |
| 202 - BUGFIX: better management of errors. Datasets remained green although the process failed | |
| 203 | |
| 204 - UPDATE: refactoring of internal management of inputs/outputs | |
| 205 | |
| 206 | |
| 207 **Version 2.0.1 - 07/06/2015** | |
| 208 | |
| 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. | |
| 210 | |
| 211 - IMPROVEMENT: parameter labels have changed to facilitate their reading. | |
| 212 | |
| 213 | |
| 214 **Version 2.0.0 - 09/06/2015** | |
| 215 | |
| 216 - NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode | |
| 217 | |
| 218 | |
| 219 ]]></help> | |
| 0 | 220 |
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221 <expand macro="citation" /> |
| 0 | 222 |
| 223 | |
| 224 </tool> | |
| 225 | |
| 226 |