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comparison DESeq_results.xml @ 6:2f8ddef8d545 draft

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update deseq2
author mingchen0919
date Tue, 07 Nov 2017 13:50:32 -0500
parents fd3514267506
children 5f7665898fd9
comparison
equal deleted inserted replaced
5:fd3514267506 6:2f8ddef8d545
1 <tool id="DESeq_results" name="DESeq2: Results" version="1.0.0"> 1 <tool id="DESeq_results" name="DESeq2: Results" version="2.0.0">
2 <requirements> 2 <requirements>
3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement> 3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
4 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
5 <requirement type="package" version="1.20.0">r-getopt</requirement> 4 <requirement type="package" version="1.20.0">r-getopt</requirement>
6 <requirement type="package" version="1.2">r-rmarkdown</requirement> 5 <requirement type="package" version="1.2">r-rmarkdown</requirement>
7 <requirement type="package" version="1.8.4">r-plyr</requirement> 6 <requirement type="package" version="1.8.4">r-plyr</requirement>
7 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
8 <requirement type="package" version="1.1.0">r-stringr</requirement> 8 <requirement type="package" version="1.1.0">r-stringr</requirement>
9 <requirement type="package" version="0.4.0">r-highcharter</requirement> 9 <requirement type="package" version="0.4.0">r-highcharter</requirement>
10 <requirement type="package" version="0.2">r-dt</requirement> 10 <requirement type="package" version="0.2">r-dt</requirement>
11 <requirement type="package" version="1.4.2">r-reshape2</requirement> 11 <requirement type="package" version="1.4.2">r-reshape2</requirement>
12 <requirement type="package" version="4.5.6">r-plotly</requirement> 12 <requirement type="package" version="4.5.6">r-plotly</requirement>
16 </requirements> 16 </requirements>
17 <description> 17 <description>
18 An R Markdown tool to display DESeq analysis. 18 An R Markdown tool to display DESeq analysis.
19 </description> 19 </description>
20 <stdio> 20 <stdio>
21 <regex match="Execution halted" 21 <!--redirecting stderr to a file. "XXX" is used to match with nothing so that tool running won't be interrupted during testing-->
22 source="both" 22 <regex match="XXX"
23 level="fatal" 23 source="stderr"
24 description="Execution halted." /> 24 level="warning"
25 <regex match="Error in" 25 description="Check the warnings_and_errors.txt file for more details."/>
26 source="both"
27 level="fatal"
28 description="An undefined error occured, please check your intput carefully and contact your administrator." />
29 <regex match="Fatal error"
30 source="both"
31 level="fatal"
32 description="An undefined error occured, please check your intput carefully and contact your administrator." />
33 </stdio> 26 </stdio>
34 <command> 27 <command>
35 <![CDATA[ 28 <![CDATA[
36 29
37 Rscript '${__tool_directory__}/DESeq_results_render.R' 30 Rscript '${__tool_directory__}/DESeq_results_render.R'
38 31
39 ## 1. input data 32 ## 1. input data
40 -e $echo 33 -e $echo
41 -w $deseq_workspace 34 -W $deseq_workspace
42 -c "$contrast_group" 35 -C '$contrast_factor'
43 -t $treatment 36 -T '$treatment'
44 -k $condition 37 -K '$condition'
45 38
46 #set $groups = [] 39 -M '$clustering_factors'
47 #for $c_group in $clustering_groups
48 #if str($c_group.group)
49 #set $groups = $groups + [str($c_group.group)]
50 #end if
51 #end for
52 #set $groups = ','.join($groups)
53 -m "$groups"
54 40
55 ## 2. output report and report site directory 41 ## 2. output report and report site directory
56 -o $deseq_results 42 -r $report
57 -d $deseq_results.files_path 43 -d $report.files_path
44 -s $sink_message
45 -R $deseq_results
58 46
59 ## 3. Rmd templates sitting in the tool directory 47 ## 3. Rmd templates sitting in the tool directory
60 48 -t '${__tool_directory__}/DESeq_results.Rmd'
61 ## _site.yml and index.Rmd template files
62 -D '${__tool_directory__}/DESeq_results.Rmd'
63 49
64 50
65 51
66 ]]> 52 ]]>
67 </command> 53 </command>
68 <inputs> 54 <inputs>
69 <param type="data" name="deseq_workspace" format="rdata" multiple="false" label="Workspace from tool DESeq2: DESeq" /> 55 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
70 <param type="data" name="sample_table" format="tabular" multiple="false" label="Sample table file" /> 56 label="Display analysis code in report?"/>
71 <param type="data_column" name="contrast_group" data_ref="sample_table" use_header_names="true" 57 <param type="data" name="deseq_workspace" format="rdata" multiple="false" optional="false"
72 optional="false" 58 label="Workspace from tool DESeq2: DESeq"/>
73 label="Group for result contrast" 59 <param type="text" name="contrast_factor" label="Factor" optional="false"
74 help=""/> 60 help="the name of a factor in the design formula"/>
75 <param type="text" name="treatment" label="Treatment level" /> 61 <param type="text" name="treatment" label="Treatment level" optional="false"
76 <param type="text" name="condition" label="Condition level" /> 62 help=" the name of the numerator level for the fold change"/>
77 63 <param type="text" name="condition" label="Condition level" optional="false"
78 <repeat name="clustering_groups" title="Gene clustering groups" min="1"> 64 help=" the name of the denominator level for the fold change"/>
79 <param type="data_column" name="group" data_ref="sample_table" use_header_names="true" 65 <param type="text" name="clustering_factors" title="Gene clustering factors" optional="false"
80 optional="false" 66 label="factors of interest for clustering samples and PCA plot"
81 label="A phenotype column from the sample table" /> 67 help="A single factor or multiple factors from the design formula. Multiple factors are separated by comma (,)."/>
82 </repeat>
83
84 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
85 </inputs> 68 </inputs>
86 <outputs> 69 <outputs>
87 <data name="deseq_results" format="html" label="DESeq Results" /> 70 <data format="html" name="report" label="DESeq results report on ${on_string}" />
71 <data format="txt" name="sink_message" label="Warnings and Errors on ${on_string}" from_work_dir="warnings_and_errors.txt"/>
72 <data format="csv" name="deseq_results" label="DESeq results on ${on_string}" from_work_dir="deseq_results.csv" />
88 </outputs> 73 </outputs>
89 <citations> 74 <citations>
90 <citation> 75 <citation>
91 @article{love2014moderated, 76 @article{love2014moderated,
92 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2}, 77 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
100 } 85 }
101 </citation> 86 </citation>
102 <citation type="bibtex"> 87 <citation type="bibtex">
103 @article{allaire2016rmarkdown, 88 @article{allaire2016rmarkdown,
104 title={rmarkdown: Dynamic Documents for R, 2016}, 89 title={rmarkdown: Dynamic Documents for R, 2016},
105 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff and Wickham, Hadley and Atkins, Aron and Hyndman, Rob}, 90 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
91 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
106 journal={R package version 0.9}, 92 journal={R package version 0.9},
107 volume={6}, 93 volume={6},
108 year={2016} 94 year={2016}
109 } 95 }
110 </citation> 96 </citation>
116 year={2015}, 102 year={2015},
117 publisher={CRC Press} 103 publisher={CRC Press}
118 } 104 }
119 </citation> 105 </citation>
120 <citation> 106 <citation>
121 @misc{pheatmap2015, 107 @article{love2014moderated,
122 title = {pheatmap: Pretty Heatmaps}, 108 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
123 author = {Raivo Kolde}, 109 author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
124 year = {2015}, 110 journal={Genome biology},
125 note = {R package version 1.0.8}, 111 volume={15},
126 url = {https://CRAN.R-project.org/package=pheatmap}, 112 number={12},
127 } 113 pages={550},
128 </citation> 114 year={2014},
129 <citation> 115 publisher={BioMed Central}
130 @misc{dt2016,
131 title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
132 author = {Yihui Xie},
133 year = {2016},
134 note = {R package version 0.2},
135 url = {https://CRAN.R-project.org/package=DT},
136 } 116 }
137 </citation> 117 </citation>
138 </citations> 118 </citations>
139 </tool> 119 </tool>