Mercurial > repos > lecorguille > camera_annotate
comparison abims_CAMERA_annotateDiffreport.xml @ 18:85b8351ded6c draft
planemo upload commit a57205d251bdebafdee164225fd03ac4d821e49c-dirty
| author | lecorguille |
|---|---|
| date | Wed, 06 Jul 2016 17:28:55 -0400 |
| parents | af2d29943e97 |
| children | fa663873dc54 |
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| 17:64fb820146f5 | 18:85b8351ded6c |
|---|---|
| 1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.5"> | 1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.6"> |
| 2 | 2 |
| 3 <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> | 3 <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> |
| 4 | 4 |
| 5 <macros> | 5 <macros> |
| 6 <import>macros.xml</import> | 6 <import>macros.xml</import> |
| 31 graphMethod $quick_block.graphMethod | 31 graphMethod $quick_block.graphMethod |
| 32 pval $quick_block.pval | 32 pval $quick_block.pval |
| 33 calcCiS $quick_block.calcCiS | 33 calcCiS $quick_block.calcCiS |
| 34 calcIso $quick_block.calcIso | 34 calcIso $quick_block.calcIso |
| 35 calcCaS $quick_block.calcCaS | 35 calcCaS $quick_block.calcCaS |
| 36 multiplier $quick_block.multiplier | 36 #if $quick_block.rules_block.rules_select == "FALSE" |
| 37 multiplier $quick_block.rules_block.multiplier | |
| 38 #else | |
| 39 multiplier $quick_block.rules_block.rules | |
| 40 #end if | |
| 37 #end if | 41 #end if |
| 38 | 42 |
| 39 #if $options.option == "show": | 43 #if $options.option == "show": |
| 40 runDiffreport TRUE | 44 runDiffreport TRUE |
| 41 eicmax $options.eicmax | 45 eicmax $options.eicmax |
| 92 </param> | 96 </param> |
| 93 <param name="pval" type="float" value="0.05" max="1" min="0" label="groupCorr: significant correlation threshold" help="[pval]" /> | 97 <param name="pval" type="float" value="0.05" max="1" min="0" label="groupCorr: significant correlation threshold" help="[pval]" /> |
| 94 <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation inside samples for peak grouping" help="[calcCiS]"/> | 98 <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation inside samples for peak grouping" help="[calcCiS]"/> |
| 95 <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping" help="[calcIso]"/> | 99 <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping" help="[calcIso]"/> |
| 96 <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation across samples for peak grouping" help="[calcCaS]"/> | 100 <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation across samples for peak grouping" help="[calcCaS]"/> |
| 97 <param name="multiplier" type="integer" value="3" label="findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" /> | 101 <conditional name="rules_block"> |
| 102 <param name="rules_select" type="select" label="Use a personal ruleset file"> | |
| 103 <option value="TRUE">TRUE</option> | |
| 104 <option value="FALSE" selected="true">FALSE</option> | |
| 105 </param> | |
| 106 <when value="FALSE"> | |
| 107 <param name="multiplier" type="integer" value="3" label="findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" /> | |
| 108 </when> | |
| 109 <when value="TRUE"> | |
| 110 <param name="rules" type="data" format="csv" label="findAdducts: User defined ruleset" help="[rules]" /> | |
| 111 </when> | |
| 112 </conditional> | |
| 98 </when> | 113 </when> |
| 99 <when value="TRUE"> | 114 <when value="TRUE"> |
| 100 <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" /> | 115 <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" /> |
| 101 </when> | 116 </when> |
| 102 </conditional> | 117 </conditional> |
| 103 | 118 |
| 104 | |
| 105 <!-- Annotatediffreport specific parameters --> | 119 <!-- Annotatediffreport specific parameters --> |
| 106 <conditional name="options"> | 120 <conditional name="options"> |
| 107 <param name="option" type="select" label="Number of condition"> | 121 <param name="option" type="select" label="Number of condition"> |
| 108 <option value="hide" selected="true">One condition</option> | 122 <option value="hide" selected="true">One condition</option> |
| 109 <option value="show">Two or more conditions</option> | 123 <option value="show">Two or more conditions</option> |
| 394 --------------------------------------------------- | 408 --------------------------------------------------- |
| 395 | 409 |
| 396 Changelog/News | 410 Changelog/News |
| 397 -------------- | 411 -------------- |
| 398 | 412 |
| 413 **Version 2.1.6 - 06/07/2016** | |
| 414 | |
| 415 - IMPROVEMENT: add the possibility to use defined ruleset | |
| 416 | |
| 399 **Version 2.1.5 - 21/04/2016** | 417 **Version 2.1.5 - 21/04/2016** |
| 400 | 418 |
| 401 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 | 419 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 |
| 402 | 420 |
| 403 | 421 |