Mercurial > repos > iuc > dexseq

annotate dexseq.xml @ 4:251393b72616 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
author iuc
date Tue, 11 Dec 2018 00:19:18 -0500
parents 6e8b61c54ff3
children 278b189248cd
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6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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1 <tool id="dexseq" name="DEXSeq" version="@VERSION@.0">
0
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2 <description>Determines differential exon usage from count tables</description>
4
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3 <macros>
2
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4 <import>macros.xml</import>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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5 </macros>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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6 <expand macro="requirements">
4
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
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7 <requirement type="package" version="1.20.2">r-getopt</requirement>
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
iuc
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8 <requirement type="package" version="0.2.20">r-rjson</requirement>
2
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9 </expand>
0
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10 <code file="dexseq_helper.py" />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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11 <stdio>
1
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12 <regex match="Execution halted"
4
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
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13 source="both"
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
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14 level="fatal"
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
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15 description="Execution halted." />
1
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16 <regex match="Input-Error 01"
4
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17 source="both"
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
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18 level="fatal"
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
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19 description="Error in your input parameters: Make sure you only apply factors to selected samples." />
0
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20 <regex match="Error in"
4
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
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21 source="both"
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
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22 level="fatal"
251393b72616 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 56ac32067af9f3cd721a4caee469207b21bb3abf
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23 description="An undefined error occured, please check your input carefully and contact your administrator." />
0
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24 <regex match="Error:"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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25 source="both"
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26 level="fatal"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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27 description="Error in the R script." />
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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28 </stdio>
2
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29 <version_command><![CDATA[
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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30 echo $(R --version | grep version | grep -v GNU)", DEXSeq version" $(R --vanilla --slave -e "library(DEXSeq); cat(sessionInfo()\$otherPkgs\$DEXSeq\$Version)" 2> /dev/null | grep -v -i "WARNING: ")" (depends on DESeq2 "$(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$Version)" 2> /dev/null | grep -v -i "WARNING: ")")"
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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31 ]]></version_command>
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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32 <command><![CDATA[
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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33 mkdir ./html_out &&
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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34 #import json
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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35 Rscript '$__tool_directory__/dexseq.R'
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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36 -o '$dexseq_out'
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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37 -p \${GALAXY_SLOTS:-4}
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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38 #set $temp_factor_names = list()
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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39 #for $factor in $rep_factorName:
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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40 #set $temp_factor = list()
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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41 #set $count_files1 = list()
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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42 #for $file in $factor.countFiles1:
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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43 $count_files1.append(str($file))
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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44 #end for
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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45 $temp_factor.append( {str($factor.factorLevel1): $count_files1} )
0
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46
2
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47 #set $count_files2 = list()
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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48 #for $file in $factor.countFiles2:
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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49 $count_files2.append(str($file))
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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50 #end for
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51 $temp_factor.append( {str($factor.factorLevel2): $count_files2} )
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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52 $temp_factor_names.append([str($factor.factorName), $temp_factor])
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53 #end for
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54 -f '#echo json.dumps(temp_factor_names)#'
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55 -a $gtf
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56 -c $fdr_cutoff
0
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57
2
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58 #if $report:
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59 -r ./html_out
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60 &&
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61 mkdir '$htmlreport.extra_files_path'
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62 &&
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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63 cp ./html_out/testForDEU.html $htmlreport
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64 &&
6e8b61c54ff3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 0a56599c36b4968095ec5a3cb589f94fb139466c
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65 cp -r ./html_out/* '$htmlreport.extra_files_path'
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66 #end if
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67 ]]></command>
0
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68 <inputs>
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69 <param name="gtf" type="data" format="gtf,gff" label="GTF file created from DEXSeq-Count tool"/>
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70 <repeat name="rep_factorName" title="Factor" min="1">
1
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71 <param name="factorName" type="text" value="FactorName" label="Specify a factor name"
0
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72 help="Only letters, numbers and underscores will be retained in this field">
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73 <sanitizer>
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74 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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75 </sanitizer>
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76 </param>
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77 <param name="factorLevel1" type="text" value="FactorLevel1" label="Specify a factor level"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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78 help="Only letters, numbers and underscores will be retained in this field">
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79 <sanitizer>
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80 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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81 </sanitizer>
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82 </param>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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83 <param name="countFiles1" type="data" format="tabular" multiple="true" label="Count file for factor level 1"/>
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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84
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85 <param name="factorLevel2" type="text" value="FactorLevel2" label="Specify a factor level"
4ca0e679f21e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dexseq commit 876fc32b23d3b9c378ddbfbbba27d37d22576c85
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86 help="Only letters, numbers and underscores will be retained in this field">
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87 <sanitizer>
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88 <valid initial="string.letters,string.digits"><add value="_" /></valid>
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89 </sanitizer>
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90 </param>
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91 <param name="countFiles2" type="data" format="tabular" multiple="true" label="Count files for factor level 2"/>
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92 </repeat>
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93 <param name="report" type="boolean" truevalue="True" falsevalue="False" checked="true"
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94 label="Visualise the analysis results?"
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95 help="Output an additional HTML file." />
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96 <param name="fdr_cutoff" type="float" min="0.0" max="1.0" value="0.05" label="All the genes under this FDR threshold will be shown in the html report"/>
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97 </inputs>
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98 <outputs>
4
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99 <data name="dexseq_out" format="tabular" label="DEXSeq result file on ${on_string}" />
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100 <data name="htmlreport" format="html" label="DEXSeq report on ${on_string}">
0
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101 <filter>report is True</filter>
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102 </data>
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103 </outputs>
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104 <tests>
2
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105 <!-- Ensure default output works-->
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106 <test expect_num_outputs="1">
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107 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
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108 <repeat name="rep_factorName">
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109 <param name="factorName" value="condition"/>
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110 <param name="factorLevel1" value="knockdown"/>
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111 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
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112 <param name="factorLevel2" value="control"/>
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113 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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114 </repeat>
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115 <param name="report" value="False"/>
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116 <param name="fdr_cutoff" value="1"/>
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117 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular" compare="sim_size"/>
2
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118 </test>
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119 <!-- Ensure report works-->
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120 <test expect_num_outputs="2">
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121 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
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122 <repeat name="rep_factorName">
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123 <param name="factorName" value="Treatment"/>
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124 <param name="factorLevel1" value="knockdown"/>
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125 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
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126 <param name="factorLevel2" value="control"/>
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127 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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128 </repeat>
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129 <param name="report" value="True"/>
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130 <param name="fdr_cutoff" value="1"/>
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131 <output name="dexseq_out" file="dexseq_result.tabular" ftype="tabular" compare="sim_size"/>
2
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132 </test>
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133 <!-- Ensure two factors works-->
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134 <test expect_num_outputs="1">
0
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135 <param name="gtf" value="dexseq.gtf" ftype="gtf"/>
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136 <repeat name="rep_factorName">
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137 <param name="factorName" value="condition"/>
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138 <param name="factorLevel1" value="knockdown"/>
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139 <param name="countFiles1" value="treated1fb.txt,treated2fb.txt,treated3fb.txt" ftype="tabular"/>
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140 <param name="factorLevel2" value="control"/>
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141 <param name="countFiles2" value="untreated1fb.txt,untreated2fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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142 </repeat>
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143 <repeat name="rep_factorName">
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144 <param name="factorName" value="libtype"/>
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145 <param name="factorLevel1" value="singleend"/>
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146 <param name="countFiles1" value="treated1fb.txt,untreated1fb.txt,untreated2fb.txt" ftype="tabular"/>
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147 <param name="factorLevel2" value="pairedend"/>
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148 <param name="countFiles2" value="treated2fb.txt,treated3fb.txt,untreated3fb.txt,untreated4fb.txt" ftype="tabular"/>
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149 </repeat>
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150 <param name="report" value="False"/>
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151 <param name="fdr_cutoff" value="0.05"/>
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152 <output name="dexseq_out" file="dexseq_result_2fact.tabular" ftype="tabular" compare="sim_size"/>
0
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153 </test>
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154 </tests>
2
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155 <help><![CDATA[
0
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156 .. class:: infomark
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157
1
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158 **What it does**
0
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159
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160 Inference of differential exon usage in RNA-Seq.
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161
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162
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163 **Inputs**
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164
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165 DEXSeq_ takes count tables generated from the dexseq_count as input. Count tables must be generated for each sample individually.
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166 DEXSeq_ is capable of handling multiple factors that affect your experiment. The first factor you input is considered to be the primary
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167 factor that affects gene expressions. You can also input several secondary factors that might
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168 influence your experiment but the final output will be changes in genes due to primary factor in the presence of secondary factors. Each factor has two levels/states.
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169 You need to select an appropriate count table from your history for each factor level.
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170
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171 The following table gives some examples of factors and their levels:
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172
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173 ========= ============== ===============
1
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174 Factor Factor level 1 Factor level 2
0
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175 --------- -------------- ---------------
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176 condition Knockdown Wildtype
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178 treatment Treated Untreated
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180 timePoint Day4 Day1
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182 SeqType SingleEnd PairedEnd
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184 Gender Female Male
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185 ========= ============== ===============
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186
4
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187 *Note*: Output log2 fold changes are based on primary factor level 1 vs. factor level 2. Here the order of factor levels is important. For example, for the factor 'condition' given in the above table, DEXSeq computes fold changes of 'Knockdown' samples against 'Wildtype', i.e. the values correspond to up or down regulations of genes in Knockdown samples.
0
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188
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189 **Output**
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190
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191 DEXSeq_ generates a tabular file containing the different columns and an optional html report.
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192
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193 ====== ==========================================================
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194 Column Description
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195 ------ ----------------------------------------------------------
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196 1 Gene and exon Identifiers
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197 2 group/gene identifier
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198 3 feature/exon identifier
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199 4 mean of the counts across samples in each feature/exon
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200 5 exon dispersion estimate
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201 6 LRT statistic
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202 7 LRT p-value
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203 8 BH adjusted p-values
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204 9 exon usage coefficient factorLevel 2
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205 10 exon usage coefficient factorLevel 1
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206 11 relative exon usage fold changes
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207 12 GRanges object of the coordinates of the exon/feature
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208 13 matrix of integer counts, of each column containing a sample
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209 14 list of transcripts overlapping with the exon
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210 ====== ==========================================================
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211
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212
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213 .. _DEXSeq: http://master.bioconductor.org/packages/release/bioc/html/DEXSeq.html
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214 ]]></help>
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215 <citations>
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216 <citation type="doi">10.1101/gr.133744.111</citation>
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217 </citations>
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218 </tool>