Mercurial > repos > lecorguille > camera_annotate
diff abims_CAMERA_annotateDiffreport.xml @ 9:7da9252dd983 draft
planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
| author | lecorguille |
|---|---|
| date | Mon, 25 Apr 2016 11:06:25 -0400 |
| parents | 8c5bb7b86df9 |
| children | 8dd6f0ffa763 |
line wrap: on
line diff
--- a/abims_CAMERA_annotateDiffreport.xml Mon Feb 22 16:48:11 2016 -0500 +++ b/abims_CAMERA_annotateDiffreport.xml Mon Apr 25 11:06:25 2016 -0400 @@ -1,24 +1,16 @@ -<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.3"> +<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.5"> <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description> - <requirements> - <requirement type="package" version="3.1.2">R</requirement> - <requirement type="binary">Rscript</requirement> - <requirement type="package" version="1.44.0">xcms</requirement> - <requirement type="package" version="1.22.0">camera</requirement> - <requirement type="package" version="2.2.1">camera_w4m_script</requirement> - <requirement type="binary">CAMERA.r</requirement> - <requirement type="package" version="1.3.18">graphicsmagick</requirement> - <requirement type="binary">convert</requirement> - </requirements> - - <stdio> - <exit_code range="1:" level="fatal" /> - </stdio> + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> <command><![CDATA[ - CAMERA.r + @COMMAND_CAMERA_SCRIPT@ xfunction annotatediff image $image @@ -56,7 +48,10 @@ new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_ #end if - + #if $zip_file: + zipfile $zip_file + #end if + ]]></command> <inputs> @@ -131,7 +126,9 @@ <when value="hide"> </when> </conditional> - + + <!-- To pass planemo test --> + <param name="zip_file" type="data" format="no_unzip.zip,zip" label="Zip file" help="Use only if you get a message which say that your original zip file have been deleted on the server." /> </inputs> <outputs> @@ -143,13 +140,13 @@ <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" /> </change_format> </data> - <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True"> - <filter>(options['option'] == 'show')</filter> - </data> + <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True"> + <filter>(options['option'] == 'show')</filter> + </data> </outputs> <tests> - <test> + <!--<test> <param name="image" value="xset.group.retcor.group.fillPeaks.RData"/> <param name="convert_param" value="False"/> <param name="num_digits" value="0"/> @@ -162,26 +159,60 @@ <param name="mzabs" value="0.015"/> <param name="intval" value="into"/> <param name="max_peaks" value="100"/> - <param name="quick_block.quick" value="FALSE"/> - <param name="quick_block.polarity" value="negative"/> - <param name="quick_block.cor_eic_th" value="0.75"/> - <param name="quick_block.graphMethod" value="hcs"/> - <param name="quick_block.pval" value="0.05"/> - <param name="quick_block.calcCiS" value="True"/> - <param name="quick_block.calcIso" value="False"/> - <param name="quick_block.calcCaS" value="False"/> - <param name="quick_block.multiplier" value="3"/> - <param name="options.option" value="show"/> - <param name="options.eicmax" value="200"/> - <param name="options.eicwidth" value="200"/> - <param name="options.value" value="into"/> - <param name="options.h" value="480"/> - <param name="options.w" value="640"/> - <param name="options.mzdec" value="2"/> - <param name="options.sortpval" value="False"/> + <param name="quick_block|quick" value="FALSE"/> + <param name="quick_block|polarity" value="negative"/> + <param name="quick_block|cor_eic_th" value="0.75"/> + <param name="quick_block|graphMethod" value="hcs"/> + <param name="quick_block|pval" value="0.05"/> + <param name="quick_block|calcCiS" value="True"/> + <param name="quick_block|calcIso" value="False"/> + <param name="quick_block|calcCaS" value="False"/> + <param name="quick_block|multiplier" value="3"/> + <param name="options|option" value="show"/> + <param name="options|eicmax" value="200"/> + <param name="options|eicwidth" value="200"/> + <param name="options|value" value="into"/> + <param name="options|h" value="480"/> + <param name="options|w" value="640"/> + <param name="options|mzdec" value="2"/> + <param name="options|sortpval" value="False"/> + <param name="zip_file" value="sacuri_dir_root.zip" ftype="zip" /> <output name="variableMetadata" file="xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> <output name="datamatrix" file="xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> - <output name="rdata" file="xset.group.retcor.group.fillPeaks.annotate.negative.Rdata" /> + </test>--> + <test> + <param name="image" value="faahKO.xset.group.retcor.group.fillpeaks.RData"/> + <param name="convert_param" value="False"/> + <param name="num_digits" value="0"/> + <param name="sigma" value="6"/> + <param name="perfwhm" value="0.6"/> + <param name="maxcharge" value="3"/> + <param name="maxiso" value="4"/> + <param name="minfrac" value="0.5"/> + <param name="ppm" value="5"/> + <param name="mzabs" value="0.015"/> + <param name="intval" value="into"/> + <param name="max_peaks" value="100"/> + <param name="quick_block|quick" value="FALSE"/> + <param name="quick_block|polarity" value="negative"/> + <param name="quick_block|cor_eic_th" value="0.75"/> + <param name="quick_block|graphMethod" value="hcs"/> + <param name="quick_block|pval" value="0.05"/> + <param name="quick_block|calcCiS" value="True"/> + <param name="quick_block|calcIso" value="False"/> + <param name="quick_block|calcCaS" value="False"/> + <param name="quick_block|multiplier" value="3"/> + <param name="options|option" value="show"/> + <param name="options|eicmax" value="200"/> + <param name="options|eicwidth" value="200"/> + <param name="options|value" value="into"/> + <param name="options|h" value="480"/> + <param name="options|w" value="640"/> + <param name="options|mzdec" value="2"/> + <param name="options|sortpval" value="False"/> + <param name="zip_file" value="faahKO_reduce.zip" ftype="zip" /> + <output name="variableMetadata" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.variableMetadata.tsv" /> + <output name="datamatrix" file="faahKO.xset.group.retcor.group.fillPeaks.annotate.dataMatrix.tsv" /> </test> </tests> @@ -189,18 +220,7 @@ <help><![CDATA[ -.. class:: infomark - -**Authors** Carsten Kuhl ckuhl@ipb-halle.de, Ralf Tautenhahn rtautenh@scripps.edu, Steffen Neumann sneumann@@ipb-halle.de - -.. class:: infomark - -**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@univ-nantes.fr - part of Workflow4Metabolomics.org [W4M] - - | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool. - ---------------------------------------------------- - +@HELP_AUTHORS@ ================ CAMERA.annotate @@ -378,7 +398,17 @@ Changelog/News -------------- -**Version 2.1.3 - 10/02/2016** +**Version 2.1.5 - 21/04/2016** + +- UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0 + + +**Version 2.1.4 - 18/04/2016** + +- TEST: refactoring to pass planemo test using conda dependencies + + +**Version 2.1.3 - 10/02/2016** - BUGFIX: better management of errors. Datasets remained green although the process failed @@ -405,10 +435,7 @@ ]]></help> - <citations> - <citation type="doi">10.1021/ac202450g</citation> - <citation type="doi">10.1093/bioinformatics/btu813</citation> - </citations> + <expand macro="citation" /> </tool>