Mercurial > repos > lecorguille > camera_annotate
comparison abims_CAMERA_annotateDiffreport.xml @ 8:8c5bb7b86df9 draft
planemo upload
author | lecorguille |
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date | Mon, 22 Feb 2016 16:48:11 -0500 |
parents | d1c09fc628e5 |
children | 7da9252dd983 |
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7:9882346d42a8 | 8:8c5bb7b86df9 |
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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 && ( | |
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> |