Mercurial > repos > lecorguille > camera_annotate
diff abims_CAMERA_annotateDiffreport.xml @ 9:c02d80efba80 draft
planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
| author | lecorguille |
|---|---|
| date | Sun, 10 Apr 2016 08:14:59 -0400 |
| parents | 32b0e4bc881f |
| children | d33e0ed5f32a |
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--- a/abims_CAMERA_annotateDiffreport.xml Mon Feb 22 17:09:43 2016 -0500 +++ b/abims_CAMERA_annotateDiffreport.xml Sun Apr 10 08:14:59 2016 -0400 @@ -2,23 +2,15 @@ <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 @@ -162,26 +154,25 @@ <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"/> <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> </tests> @@ -189,18 +180,7 @@ <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 @@ -405,10 +385,7 @@ ]]></help> - <citations> - <citation type="doi">10.1021/ac202450g</citation> - <citation type="doi">10.1093/bioinformatics/btu813</citation> - </citations> + <expand macro="citation" /> </tool>