Mercurial > repos > mingchen0919 > aurora_dustmasker
comparison rmarkdown_report.Rmd @ 1:e0828838e0f3 draft default tip
update
author | mingchen0919 |
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date | Fri, 09 Nov 2018 15:25:01 -0500 |
parents | b8c76b06d724 |
children |
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0:b8c76b06d724 | 1:e0828838e0f3 |
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1 --- | 1 --- |
2 title: 'Aurora Tool Report' | 2 title: 'Dustmasker Report' |
3 output: | 3 output: |
4 html_document: | 4 html_document: |
5 highlight: pygments | 5 highlight: pygments |
6 --- | 6 --- |
7 | 7 |
52 --- | 52 --- |
53 # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE | 53 # ADD YOUR DATA ANALYSIS CODE AND MARKUP TEXT BELOW TO EXTEND THIS R MARKDOWN FILE |
54 --- | 54 --- |
55 | 55 |
56 | 56 |
57 ## Run `dustmasker` | 57 ## Run `dustmasker` job |
58 | 58 |
59 ```{bash} | 59 ```{bash echo=FALSE} |
60 dustmasker \ | 60 sh ${TOOL_INSTALL_DIR}/scripts_generator.sh |
61 -in $X_A \ | |
62 -window $X_B \ | |
63 -level $X_C \ | |
64 -linker $X_D \ | |
65 -infmt $X_E \ | |
66 -outfmt $X_F \ | |
67 | |
68 $(if [ "$X_G" = "NO_ARGUMENT_YES" ]; then echo '-parse_seqids'; fi) \ | |
69 | |
70 -out dustmasker_out | |
71 ``` | 61 ``` |
72 | 62 |
73 Options explanation: | 63 ```{r echo=FALSE,warning=FALSE,results='asis'} |
64 # display content of the job-script.sh file. | |
65 cat('```bash\n') | |
66 cat(readLines(paste0(Sys.getenv('REPORT_FILES_PATH'), '/dustmasker.sh')), sep = '\n') | |
67 cat('\n```') | |
68 ``` | |
69 | |
70 | |
71 **Options explanation:** | |
74 | 72 |
75 <pre> | 73 <pre> |
76 -in <File_In> | 74 -in <File_In> |
77 input file name | 75 input file name |
78 Default = `-' | 76 Default = `-' |
96 -parse_seqids | 94 -parse_seqids |
97 Parse Seq-ids in FASTA input | 95 Parse Seq-ids in FASTA input |
98 | 96 |
99 -out <File_Out> | 97 -out <File_Out> |
100 output file name | 98 output file name |
101 Default = `-' | |
102 </pre> | 99 </pre> |