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comparison DESeq.xml @ 6:2f8ddef8d545 draft

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update deseq2
author mingchen0919
date Tue, 07 Nov 2017 13:50:32 -0500
parents fd3514267506
children 466053167103
comparison
equal deleted inserted replaced
5:fd3514267506 6:2f8ddef8d545
1 <tool id="DESeq" name="DESeq2: DESeq" version="1.0.0"> 1 <tool id="DESeq" name="DESeq2: DESeq" version="1.0.0">
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 perform DESeq analysis. 18 An R Markdown tool to perform 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 '${__tool_directory__}/DESeq_render.R' 30 Rscript '${__tool_directory__}/DESeq_render.R'
38 31
32
39 ## 1. input data 33 ## 1. input data
40 -e $echo 34 -e $echo
41 -c $count_files 35 ##----- code chunk to get file paths and raw file names for a multiple inputs data field ----
42 -s $sample_table 36 #set $sep = ''
43 -p "$design_formula" 37 #set $count_file_paths = ''
38 #set $count_file_names = ''
39 #for $count_file in $count_files:
40 #set $count_file_paths += $sep + str($count_file)
41 #set $count_file_names += $sep + str($count_file.name)
42 #set $sep = ','
43 #end for
44 ##----------------- end for getting file names and file paths ------------------------------
45 -P '$count_file_paths'
46 -N '$count_file_names'
47 -S $sample_table
48 -p '$design_formula'
44 49
45 ## 2. output report and report site directory 50 ## 2. output report and report site directory
46 -o $DESeq 51 -r $report
47 -d $DESeq.files_path 52 -d $report.files_path
53 -s $sink_message
48 -w $deseq_workspace 54 -w $deseq_workspace
49 55
50 ## 3. Rmd templates sitting in the tool directory 56 ## 3. Rmd templates from the tool directory
51 57 -t '${__tool_directory__}/DESeq.Rmd'
52 ## _site.yml and index.Rmd template files
53 -D '${__tool_directory__}/DESeq.Rmd'
54 58
55 59
56 60
57 ]]> 61 ]]>
58 </command> 62 </command>
59 <inputs> 63 <inputs>
60 <param type="data" name="count_files" format="tabular" multiple="true" label="Count files from htseq-count" /> 64 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
65 label="Display analysis code in report?"/>
66 <param type="data" name="count_files" format="tabular" multiple="true" label="Count files from htseq-count"/>
61 <param type="data" name="sample_table" format="tabular" multiple="false" label="sample table file" 67 <param type="data" name="sample_table" format="tabular" multiple="false" label="sample table file"
62 help="The sample table file contains a table. The first column is the sample name, the second column is 68 help="The sample table file contains a table. The first column is the sample name, the second column is
63 the count file name and the rest of columns are treatment columns. The file names in this table have 69 the count file name and the rest of columns are treatment columns. The file names in this table have
64 to be in the same order as the count files uploaded in the previous step. "/> 70 to be in the same order as the count files uploaded in the previous step. "/>
65 <param type="text" name="design_formula" value="~ condition_1 + condition_2" label="Design formula" 71 <param type="text" name="design_formula" value="~ condition_1 + condition_2" label="Design formula"
70 <add preset="string.printable"/> 76 <add preset="string.printable"/>
71 <add value="~"/> 77 <add value="~"/>
72 </valid> 78 </valid>
73 </sanitizer> 79 </sanitizer>
74 </param> 80 </param>
75 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
76 </inputs> 81 </inputs>
77 <outputs> 82 <outputs>
78 <data name="DESeq" format="html" label="DESeq Analysis" /> 83 <data name="report" format="html" label="DESeq Analysis on ${on_string}"/>
79 <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis" /> 84 <data format="txt" name="sink_message" label="Warnings and Errors on ${on_string}" from_work_dir="warnings_and_errors.txt"/>
85 <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis on ${on_string}"/>
80 </outputs> 86 </outputs>
81 <citations> 87 <citations>
82 <citation> 88 <citation>
83 @article{love2014moderated, 89 @article{love2014moderated,
84 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2}, 90 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
92 } 98 }
93 </citation> 99 </citation>
94 <citation type="bibtex"> 100 <citation type="bibtex">
95 @article{allaire2016rmarkdown, 101 @article{allaire2016rmarkdown,
96 title={rmarkdown: Dynamic Documents for R, 2016}, 102 title={rmarkdown: Dynamic Documents for R, 2016},
97 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}, 103 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
104 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
98 journal={R package version 0.9}, 105 journal={R package version 0.9},
99 volume={6}, 106 volume={6},
100 year={2016} 107 year={2016}
101 } 108 }
102 </citation> 109 </citation>
108 year={2015}, 115 year={2015},
109 publisher={CRC Press} 116 publisher={CRC Press}
110 } 117 }
111 </citation> 118 </citation>
112 <citation> 119 <citation>
113 @misc{pheatmap2015, 120 @article{love2014moderated,
114 title = {pheatmap: Pretty Heatmaps}, 121 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
115 author = {Raivo Kolde}, 122 author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
116 year = {2015}, 123 journal={Genome biology},
117 note = {R package version 1.0.8}, 124 volume={15},
118 url = {https://CRAN.R-project.org/package=pheatmap}, 125 number={12},
119 } 126 pages={550},
120 </citation> 127 year={2014},
121 <citation> 128 publisher={BioMed Central}
122 @misc{dt2016,
123 title = {DT: A Wrapper of the JavaScript Library 'DataTables'},
124 author = {Yihui Xie},
125 year = {2016},
126 note = {R package version 0.2},
127 url = {https://CRAN.R-project.org/package=DT},
128 } 129 }
129 </citation> 130 </citation>
130 </citations> 131 </citations>
131 </tool> 132 </tool>