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comparison galaxy/wrappers/ExprQCplots.xml @ 1:0435f94d27a7 draft

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"planemo upload for repository https://github.com/juliechevalier/GIANT/tree/master commit e2b27d6ff2eab66454f984dbf1a519192f41db97"
author vandelj
date Wed, 09 Sep 2020 10:28:54 +0000
parents 488e6e8bb8cb
children
comparison
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0:488e6e8bb8cb 1:0435f94d27a7
1 <tool name="GIANT-QC Plots" id="giant_plot_functions" version="0.1.3"> 1 <tool name="GIANT-QC Plots" id="giant_plot_functions" version="0.1.4">
2 <description>Descriptive plots of .CEL collections or normalized expression data</description> 2 <description>Descriptive plots of .CEL collections or normalized expression data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.40.1">bioconductor-oligo</requirement> 4 <requirement type="package" version="1.40.1">bioconductor-oligo</requirement>
5 <requirement type="package" version="2.2_13">r-ff</requirement> 5 <requirement type="package" version="2.2_13">r-ff</requirement>
6 <requirement type="package" version="2.2.1">r-ggplot2</requirement> 6 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
7 <requirement type="package" version="4.5.6">r-plotly</requirement> 7 <requirement type="package" version="4.5.6">r-plotly</requirement>
8 <requirement type="package" version="1.8_17">r-mgcv</requirement> 8 <requirement type="package" version="1.8_17">r-mgcv</requirement>
9 </requirements> 9 </requirements>
10 <code file="../../src/General_functions.py"/> 10 <code file="../../src/General_functions.py"/>
11 <!--<code file="./src/General_functions.py"/> change for Planemo test-->
11 <stdio> 12 <stdio>
12 <regex match="Execution halted" 13 <regex match="Execution halted"
13 source="both" 14 source="both"
14 level="fatal" 15 level="fatal"
15 description="Execution halted, please contact tool developer or administrators." /> 16 description="Execution halted, please contact tool developer or administrators." />
20 <exit_code range="15" level="fatal" description="Error during formating scripts, see log file for more information." /> 21 <exit_code range="15" level="fatal" description="Error during formating scripts, see log file for more information." />
21 <exit_code range="10" level="fatal" description="Missing file during html report, see log file for more information." /> 22 <exit_code range="10" level="fatal" description="Missing file during html report, see log file for more information." />
22 <exit_code range="1:9" level="fatal" description="Error in R execution, see log file for more information." /> 23 <exit_code range="1:9" level="fatal" description="Error in R execution, see log file for more information." />
23 </stdio> 24 </stdio>
24 <command> <![CDATA[ 25 <command> <![CDATA[
25 ##set $dataType=$dataFile.extension 26 ##set $dataType=$inputData.extension
26 #set $dataType=$dataFile[0].ext 27 #set $dataType=$inputData[0].ext
27 28
28 #if $conditionInformation and $pcaSection.factorsToInclude!="None": 29 #if $conditionInformation and $pcaSection.factorsToInclude!="None":
29 bash $scriptPrepareTable; 30 bash $scriptPrepareTable;
30 ret_code=\$?; 31 ret_code=\$?;
31 if [ \$ret_code != 0 ]; then 32 if [ \$ret_code != 0 ]; then
32 exit \$ret_code; 33 exit \$ret_code;
33 fi; 34 fi;
34 #end if 35 #end if
35 36
36 #if ($dataType == "cel" and len($dataFile)>1) or ($dataType == "tabular" and len($dataFile)==1): 37 #if ($dataType == "cel" and len($inputData)>1) or ($dataType == "tabular" and len($inputData)==1):
37 Rscript '$__tool_directory__/../../src/ExprPlotsScript.R' -i '$dataFile' -l '$log' -f '$advSection.imageFormat' -j '$dataType' 38 Rscript '$__tool_directory__/../../src/ExprPlotsScript.R' -i '$inputData' -l '$log' -f '$advSection.imageFormat' -j '$dataType'
39 ##change for Planemo test
40 ##Rscript '$__tool_directory__/src/ExprPlotsScript.R' -i '$inputData' -l '$log' -f '$advSection.imageFormat' -j '$dataType'
38 #if $dataType == "cel": 41 #if $dataType == "cel":
39 #for $inputDataset in $dataFile 42 #for $inputDataset in $inputData
40 -c '${inputDataset.name}' 43 -c '${inputDataset.name}'
41 #end for 44 #end for
42 #end if 45 #end if
43 #if $conditionInformation and $pcaSection.factorsToInclude!="None": 46 #if $conditionInformation and $pcaSection.factorsToInclude!="None":
44 -t 'factorTable.csv' 47 -t 'factorTable.csv'
93 ]]> 96 ]]>
94 </configfile> 97 </configfile>
95 98
96 <configfile name="scriptTransfer"> 99 <configfile name="scriptTransfer">
97 <![CDATA[ 100 <![CDATA[
98 #set $dataType=$dataFile[0].ext 101 #set $dataType=$inputData[0].ext
99 #set $cnt=1 102 #set $cnt=1
100 103
101 ##create header of HTML file 104 ##create header of HTML file
102 printf "<!DOCTYPE html>\n<html>\n" > $html_file 105 printf "<!DOCTYPE html>\n<html>\n" > $html_file
103 106
379 382
380 383
381 <inputs> 384 <inputs>
382 <param type="text" name="title" value="PlotFigure_toPersonalize" label="Title for output"> 385 <param type="text" name="title" value="PlotFigure_toPersonalize" label="Title for output">
383 </param> 386 </param>
384 <param type="data" name="dataFile" format="cel,tabular" label="Select one .CEL collection or one tabular file" optional="false" multiple="true" > 387 <param type="data" name="inputData" format="cel,tabular" label="Select one .CEL collection or one tabular file" optional="false" multiple="true" >
385 </param> 388 </param>
386 389
387 <section name="plotSection" title="Plots selection" expanded="True"> 390 <section name="plotSection" title="Plots selection" expanded="True">
388 <param type="boolean" name="histogramToPlot" checked="true" label="Plot histograms" help="Plot intensity distribution for each condition (pm probes for .cel)"> 391 <param type="boolean" name="histogramToPlot" checked="true" label="Plot histograms" help="Plot intensity distribution for each condition (pm probes for .cel)">
389 </param> 392 </param>
394 <param type="boolean" name="microarrayToPlot" checked="true" label="Display microarray images (only for .CEL files)"> 397 <param type="boolean" name="microarrayToPlot" checked="true" label="Display microarray images (only for .CEL files)">
395 </param> 398 </param>
396 399
397 </section> 400 </section>
398 <section name="pcaSection" title="PCA analysis" expanded="True"> 401 <section name="pcaSection" title="PCA analysis" expanded="True">
399 <param type="boolean" name="acpToPlot" checked="true" label="Plot 3D PCA" help="3D plot of conditions in the space defined by the 3 principal components"> 402 <param type="boolean" name="acpToPlot" checked="true" label="Plot 3D PCA" help="3D plot of conditions in the space defined by the 3 principal components">
400 </param> 403 </param>
401 <param type="data" name="conditionInformation" format="tabular" label="Factor information tabular file (optional)" optional="true" multiple="false"> 404 <param type="data" name="conditionInformation" format="tabular" label="Factor information tabular file (optional)" optional="true" multiple="false">
402 </param> 405 </param>
403 <param name="factorsToInclude" type="select" optional="true" multiple="true" label="Select factor informations to display (optional)" 406 <param name="factorsToInclude" type="select" optional="true" multiple="true" label="Select factor informations to display (optional)"
404 refresh_on_change="true" dynamic_options="get_column_names(pcaSection['conditionInformation'].file_name,0)"> 407 refresh_on_change="true" dynamic_options="get_column_names(pcaSection['conditionInformation'].file_name,0)">
440 <filter>plotSection['boxplotToPlot']</filter> 443 <filter>plotSection['boxplotToPlot']</filter>
441 </collection> 444 </collection>
442 445
443 <collection name="outputMicroarrayList" label="${title}_MicroarrayList" type="list"> 446 <collection name="outputMicroarrayList" label="${title}_MicroarrayList" type="list">
444 <discover_datasets pattern="(?P&lt;designation&gt;Microarray\_.*)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/> 447 <discover_datasets pattern="(?P&lt;designation&gt;Microarray\_.*)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/>
445 <filter>plotSection['microarrayToPlot'] and dataFile[0].ext == "cel"</filter> 448 <filter>plotSection['microarrayToPlot'] and inputData[0].ext == "cel"</filter>
446 </collection> 449 </collection>
447 450
448 <collection name="outputPCAList" label="${title}_PCA" type="list"> 451 <collection name="outputPCAList" label="${title}_PCA" type="list">
449 <discover_datasets pattern="(?P&lt;designation&gt;PCA[0-9]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/> 452 <discover_datasets pattern="(?P&lt;designation&gt;PCA[0-9]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/>
450 <discover_datasets pattern="(?P&lt;designation&gt;screePlot)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/> 453 <discover_datasets pattern="(?P&lt;designation&gt;screePlot)\.(?P&lt;ext&gt;[^\._]+)?" directory="plotDir" visible="false"/>
456 459
457 460
458 461
459 <tests> 462 <tests>
460 <test maxseconds="3600"> 463 <test maxseconds="3600">
461 <param name="wfile" value="wiggle.wig" /> 464 <param name="inputData" value="./NormalizedData.tabular" />
462 <param name="bfile" value="bedfile.bed" /> 465 <section name="plotSection" >
463 <param name="span" value="3000" /> 466 <param name="histogramToPlot" value="true" />
464 <param name="pfres" value="50" /> 467 <param name="maplotToPlot" value="true" />
465 <param name="lowersize" value="1000" /> 468 <param name="boxplotToPlot" value="true" />
466 <param name="middlesize" value="2000" /> 469 <param name="microarrayToPlot" value="false" />
467 <param name="uppersize" value="3000" /> 470 </section>
468 <param name="lowerbisize" value="2500" /> 471 <section name="pcaSection" >
469 <param name="upperbisize" value="5000" /> 472 <param name="acpToPlot" value="true" />
470 <param name="reldist" value="3000" /> 473 <param name="conditionInformation" value="./FactorFileGenerator/output/conditionsFile.csv" />
471 <param name="genome" value="hg18" /> 474 <param name="factorsToInclude" value="Strain,Treatment" />
472 <param name="imagetype" value="PDF" /> 475 </section>
473 <param name="enable" value="no" /> 476 <section name="advSection" >
474 <output name="log" file="ceas_1/ceas_1.pdf" /> 477 <param name="imageFormat" value="png" />
478 <param name="imagePlotlyFormat" value="png" />
479 </section>
480 <output name="html_file" file="./ExprQCplots/output/outputHTML.zip" decompress="true" >
481 </output>
482 <output name="log" file="./ExprQCplots/output/outputLog.txt" compare="sim_size" delta_frac="0.10" />
475 </test> 483 </test>
476 </tests> 484 </tests>
477 485
478 486
479 487