Mercurial > repos > lecorguille > camera_annotate

comparison abims_CAMERA_annotateDiffreport.xml @ 8:8c5bb7b86df9 draft

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planemo upload
author lecorguille
date Mon, 22 Feb 2016 16:48:11 -0500
parents d1c09fc628e5
children 7da9252dd983
comparison
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7:9882346d42a8 8:8c5bb7b86df9
1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.0"> 1 <tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.3">
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 <requirements> 5 <requirements>
6 <requirement type="package" version="3.1.2">R</requirement> 6 <requirement type="package" version="3.1.2">R</requirement>
7 <requirement type="binary">Rscript</requirement> 7 <requirement type="binary">Rscript</requirement>
8 <requirement type="package" version="1.44.0">xcms</requirement> 8 <requirement type="package" version="1.44.0">xcms</requirement>
9 <requirement type="package" version="1.22.0">camera</requirement> 9 <requirement type="package" version="1.22.0">camera</requirement>
10 <requirement type="package" version="2.1">camera_w4m_script</requirement> 10 <requirement type="package" version="2.2.1">camera_w4m_script</requirement>
11 <requirement type="binary">CAMERA.r</requirement>
12 <requirement type="package" version="1.3.18">graphicsmagick</requirement>
13 <requirement type="binary">convert</requirement>
11 </requirements> 14 </requirements>
12 15
13 <stdio> 16 <stdio>
14 <exit_code range="1:" level="fatal" /> 17 <exit_code range="1:" level="fatal" />
15 </stdio> 18 </stdio>
16 19
17 <command interpreter="Rscript"> 20 <command><![CDATA[
18 CAMERA.r 21 CAMERA.r
19 xfunction annotatediff image $image 22 xfunction annotatediff
20 convert_param $convert_param num_digits $num_digits nSlaves \${GALAXY_SLOTS:-1} 23 image $image
24
25 variableMetadataOutput $variableMetadata
26 dataMatrixOutput $datamatrix
27 xsetRdataOutput $rdata
28
29 convert_param $convert_param num_digits $num_digits
30 nSlaves \${GALAXY_SLOTS:-1}
21 sigma $sigma perfwhm $perfwhm 31 sigma $sigma perfwhm $perfwhm
22 maxcharge $maxcharge maxiso $maxiso minfrac $minfrac 32 maxcharge $maxcharge maxiso $maxiso minfrac $minfrac
23 ppm $ppm mzabs $mzabs intval $intval 33 ppm $ppm mzabs $mzabs intval $intval
24 max_peaks $max_peaks 34 max_peaks $max_peaks
25 quick $quick_block.quick 35 quick $quick_block.quick
33 calcCaS $quick_block.calcCaS 43 calcCaS $quick_block.calcCaS
34 multiplier $quick_block.multiplier 44 multiplier $quick_block.multiplier
35 #end if 45 #end if
36 46
37 #if $options.option == "show": 47 #if $options.option == "show":
48 runDiffreport TRUE
38 eicmax $options.eicmax 49 eicmax $options.eicmax
39 eicwidth $options.eicwidth 50 eicwidth $options.eicwidth
40 value $options.value 51 value $options.value
41 sortpval $options.sortpval 52 sortpval $options.sortpval
42 h $options.h 53 h $options.h
43 w $options.w 54 w $options.w
44 mzdec $options.mzdec 55 mzdec $options.mzdec
45 #else 56 new_file_path ${__new_file_path__}/primary_${output_diffreport.id}_
46 eicmax 0
47 eicwidth 200
48 value "into"
49 sortpval TRUE
50 h 480
51 w 640
52 mzdec 2
53 #end if 57 #end if
54 &amp;&amp; (
55 mv variableMetadata.tsv $variableMetadata;
56 mv dataMatrix.tsv $datamatrix;
57 mv annotatediff.RData $rdata
58 );
59 cat xset.log
60 58
61 59
62 </command> 60 ]]></command>
63 61
64 <inputs> 62 <inputs>
65 63
66 64
67 <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" /> 65 <param name="image" type="data" label="RData file" format="rdata.xcms.fillpeaks,rdata" help="output file from another function xcms (fillPeaks)" />
143 <change_format> 141 <change_format>
144 <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" /> 142 <when input="quick_block.polarity" value="positive" format="rdata.camera.positive" />
145 <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" /> 143 <when input="quick_block.polarity" value="negative" format="rdata.camera.negative" />
146 </change_format> 144 </change_format>
147 </data> 145 </data>
148 <data name="output_zip" format="zip" from_work_dir="Xdiffreport.zip" label="${image.name[:-6]}.annotateDiffreport.zip" > 146 <data name="output_diffreport" format="text" label="${image.name[:-6]}.annotateDiffreport" hidden="True">
149 <filter>(options['option'] == 'show')</filter> 147 <filter>(options['option'] == 'show')</filter>
150 </data> 148 </data>
151 </outputs> 149 </outputs>
152 150
153 <tests> 151 <tests>
187 </test> 185 </test>
188 </tests> 186 </tests>
189 187
190 188
191 189
192 <help> 190 <help><![CDATA[
193 191
194 .. class:: infomark 192 .. class:: infomark
195 193
196 **Authors** Carsten Kuhl ckuhl@ipb-halle.de, Ralf Tautenhahn rtautenh@scripps.edu, Steffen Neumann sneumann@@ipb-halle.de 194 **Authors** Carsten Kuhl ckuhl@ipb-halle.de, Ralf Tautenhahn rtautenh@scripps.edu, Steffen Neumann sneumann@@ipb-halle.de
197 195
372 370
373 **Example of a part of xset.annotate.variableMetadata.tsv output** 371 **Example of a part of xset.annotate.variableMetadata.tsv output**
374 372
375 .. image:: annotatediffreport_variableMetadata.png 373 .. image:: annotatediffreport_variableMetadata.png
376 374
377 </help> 375
376 ---------------------------------------------------
377
378 Changelog/News
379 --------------
380
381 **Version 2.1.3 - 10/02/2016**
382
383 - BUGFIX: better management of errors. Datasets remained green although the process failed
384
385 - BUGFIX: the conversion into minutes of the retention time was applied to the diffreport outputs (several conditions)
386
387 - IMPROVEMENT: when there are several conditions, the tool will generate individual datasets (tsv, pdf) instead of a zip file. The usual png (eic, boxplot) will from now be integrated in two pdf.
388
389 - UPDATE: refactoring of internal management of inputs/outputs
390
391
392 VERSION 2.1.0 - 09/10/2015**
393
394 - BUGFIX: There was a bug with the CAMERA.annotate (generating a bad dataMatrix (intensities which don't match with the metabolites))
395
396
397 VERSION 2.1.0 - 07/06/2015**
398
399 - 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.
400
401 - IMPROVEMENT: parameter labels have changed to facilitate their reading.
402
403 - UPDATE: merged with annotateDiffreport. Some parameters are dedicated to experiences with several conditions
404
405
406 ]]></help>
378 407
379 <citations> 408 <citations>
380 <citation type="doi">10.1021/ac202450g</citation> 409 <citation type="doi">10.1021/ac202450g</citation>
381 <citation type="doi">10.1093/bioinformatics/btu813</citation> 410 <citation type="doi">10.1093/bioinformatics/btu813</citation>
382 </citations> 411 </citations>