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comparison DESeq.xml @ 0:6f94b4b9de44 draft

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author mingchen0919
date Tue, 27 Feb 2018 23:57:53 -0500
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-1:000000000000 0:6f94b4b9de44
1 <tool name="DESeq2: Analysis" id='deseq2' version="2.0.1">
2 <description>
3 perform differential expression analysis
4 </description>
5 <requirements>
6 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
7 <requirement type="package" version="1.20.0">r-getopt</requirement>
8 <requirement type="package" version="1.6">r-rmarkdown</requirement>
9 <requirement type="package" version="1.14.1">bioconductor-deseq2</requirement>
10 <requirement type="package" version="0.2">r-dt</requirement>
11 <requirement type="package" version="1.0.8">r-pheatmap</requirement>
12 </requirements>
13 <stdio>
14 <regex match="XXX" source="stderr" level="warning"
15 description="Check the warnings_and_errors.txt file for more details."/>
16 </stdio>
17 <command><![CDATA[
18
19
20 Rscript '${__tool_directory__}/DESeq_render.R'
21
22 -e $echo
23
24 -o $report
25 -d $report.files_path
26 -s $sink_message
27 -t '${__tool_directory__}'
28
29
30 ##----- code chunk to get file paths and raw file names for a multiple inputs data field ----
31 #set $sep = ''
32 #set $count_file_paths = ''
33 #set $count_file_names = ''
34 #for $count_file in $count_files:
35 #set $count_file_paths += $sep + str($count_file)
36 #set $count_file_names += $sep + str($count_file.name)
37 #set $sep = ','
38 #end for
39 ##----------------- end for getting file names and file paths ------------------------------
40 -P '$count_file_paths'
41 -N '$count_file_names'
42 -S $sample_table
43 -p '$design_formula'
44 -w $deseq_workspace
45
46
47 ]]></command>
48 <inputs>
49 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
50 label="Display analysis code in report?"/>
51 <param type="data" name="count_files" format="txt" multiple="true" label="Count files from htseq-count"/>
52 <param type="data" name="sample_table" format="txt" multiple="false" label="sample table file"
53 help="The sample table file contains a table. The first column is the sample name, the second column is
54 the count file name and the rest of columns are treatment columns. The file names in this table have
55 to be in the same order as the count files uploaded in the previous step. "/>
56 <param type="text" name="design_formula" value="~ condition_1 + condition_2" label="Design formula"
57 help="The simplest design formula for differential expression would be ~ condition, where condition
58 is a column in colData(dds) that specifies which of two (or more groups) the samples belong to">
59 <sanitizer>
60 <valid initial="default">
61 <add preset="string.printable"/>
62 <add value="~"/>
63 </valid>
64 </sanitizer>
65 </param>
66 </inputs>
67 <outputs>
68 <data name="report" format="html" label="DESeq Analysis on ${on_string}"/>
69 <data format="txt" name="sink_message" label="Warnings and Errors on"
70 from_work_dir="warnings_and_errors.txt"/>
71 <data name="deseq_workspace" format="rdata" label="R workspace: DESeq analysis on ${on_string}"/>
72 </outputs>
73 <citations>
74 <citation type="bibtex">
75 @article{love2014moderated,
76 title={Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2},
77 author={Love, Michael I and Huber, Wolfgang and Anders, Simon},
78 journal={Genome biology},
79 volume={15},
80 number={12},
81 pages={550},
82 year={2014},
83 publisher={BioMed Central}
84 }
85 </citation>
86 <citation type="bibtex"><![CDATA[
87 @article{allaire2016rmarkdown,
88 title={rmarkdown: Dynamic Documents for R, 2016},
89 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
90 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
91 journal={R package version 0.9},
92 volume={6},
93 year={2016}
94 }
95 ]]></citation>
96 <citation type="bibtex"><![CDATA[
97 @book{xie2015dynamic,
98 title={Dynamic Documents with R and knitr},
99 author={Xie, Yihui},
100 volume={29},
101 year={2015},
102 publisher={CRC Press}
103 }
104 ]]></citation>
105 </citations>
106 </tool>