Mercurial > repos > lecorguille > camera_annotate
changeset 27:75a1b3f7bacc draft default tip
planemo upload commit 24d44ee26b7c23380c2b42fae2f7f6e58472100d
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--- a/macros.xml Mon Sep 30 12:22:28 2024 +0000 +++ b/macros.xml Sun Nov 24 21:27:48 2024 +0000 @@ -37,9 +37,9 @@ <xml name="input_file_load"> <section name="file_load_section" title="Resubmit your raw dataset or your zip file"> <conditional name="file_load_conditional"> - <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server." > - <option value="no" >no need</option> - <option value="yes" >yes</option> + <param name="file_load_select" type="select" label="Resubmit your dataset or your zip file" help="Use only if you get a message which say that your original dataset or zip file have been deleted on the server."> + <option value="no">no need</option> + <option value="yes">yes</option> </param> <when value="no"> </when> @@ -68,6 +68,15 @@ </section> </xml> + <xml name="test_file_load_faahKO_15"> + <section name="file_load_section"> + <conditional name="file_load_conditional"> + <param name="file_load_select" value="yes" /> + <param name="input" value="wt15.CDF,ko15.CDF" ftype="netcdf" /> + </conditional> + </section> + </xml> + <!-- peaklist export option management --> <token name="@COMMAND_PEAKLIST@"> convertRTMinute $export.convertRTMinute @@ -83,7 +92,7 @@ <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" /> <param name="intval" type="select" label="General used intensity value" help="[intval] See the help section below"> <option value="into" selected="true">into</option> - <option value="maxo" >maxo</option> + <option value="maxo">maxo</option> <option value="intb">intb</option> </param> </section> @@ -115,18 +124,18 @@ <param name="max_peaks" value="100"/> </section> <section name="diffreport"> - <conditional name="options"> - <param name="option" value="show"/> - <param name="eicmax" value="200"/> - <param name="eicwidth" value="200"/> - <param name="value" value="into"/> - <param name="h" value="480"/> - <param name="w" value="640"/> - <param name="mzdec" value="2"/> - <param name="sortpval" value="False"/> - <param name="tabular2" value="zip"/> - <param name="png2" value="zip"/> - </conditional> + <conditional name="options"> + <param name="option" value="show"/> + <param name="eicmax" value="200"/> + <param name="eicwidth" value="200"/> + <param name="value" value="into"/> + <param name="h" value="480"/> + <param name="w" value="640"/> + <param name="mzdec" value="2"/> + <param name="sortpval" value="False"/> + <param name="tabular2" value="zip"/> + <param name="png2" value="zip"/> + </conditional> </section> <expand macro="test_peaklist"/> </xml> @@ -164,6 +173,12 @@ </token> + <token name="@HELP_CAMERA_SUITE@"> +**Version 0.1.0+camera1.48.0 - 06/11/2024** + +- Initial release with core functionalities for peak annotation, grouping, and visualization using CAMERA (see CAMERA News_). + </token> + <token name="@HELP_CAMERA_NEWVERSION_1480@"> **Version 2.2.6+camera1.48.0 - 11/06/2021** @@ -188,4 +203,15 @@ <citation type="doi">10.1093/bioinformatics/btu813</citation> </citations> </xml> + + <xml name="creator"> + <creator> + <organization name="MELISA" url="https://www.laberca.org/plateforme-melisa/presentation"></organization> + <organization name="Workflow4metabolomics" url="https://workflow4metabolomics.org/"></organization> + + <person givenName="Yann" familyName="Guitton" url="https://github.com/yguitton"></person> + <person givenName="Damien" familyName="Rat" url="https://github.com/DamienCode404"></person> + <person givenName="Julien" familyName="Saint-Vanne" url="https://github.com/jsaintvanne"></person> + </creator> + </xml> </macros>
Binary file test-data/xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.findIsotopes.RData has changed
Binary file test-data/xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.findIsotopes.findAdducts.RData has changed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/xset.merged.group.retcor.group.fillPeaks.fwhm.groupCorr.findIsotopes.findAdducts.variableMetadata.tsv Sun Nov 24 21:27:48 2024 +0000 @@ -0,0 +1,559 @@ +name name_custom mz mzmin mzmax rt rtmin rtmax npeaks KO WT ms_level isotopes adduct pcgroup +M200T2927 M200.1000T2927.0754 200.100006103516 200.100006103516 200.100006103516 2927.0753901825 2925.9079491655 2928.24283119951 2 1 1 1 43 +M201T2531 M201.0465T2531.1252 201.046529396752 201.029215881161 201.063842912344 2531.12516042043 2531.08932212593 2531.16099871493 2 1 1 1 129 +M205T2785 M205.0000T2785.4174 205 205 205 2785.41742651204 2784.87633345166 2785.95851957242 2 1 1 1 9 +M206T2785 M205.9839T2785.4105 205.98390828422 205.981949731978 205.985866836462 2785.41047994888 2784.38647613272 2786.43448376505 2 1 1 1 9 +M207T2713 M207.0807T2712.6530 207.080666733779 207.079243388168 207.082090079391 2712.65296577754 2712.41726475728 2712.8886667978 2 1 1 1 64 +M208T2641 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