Mercurial > repos > mingchen0919 > aurora_star_site

annotate rmarkdown_report.xml @ 4:804fe260ee6c draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
author mingchen0919
date Sun, 30 Dec 2018 14:04:22 -0500
parents c8c0b708c221
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
1 <tool name="aurora_star_site" id='aurora_star_site_report' version="2.0.1">
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
2 <description>
1
c8c0b708c221 planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b-dirty
mingchen0919
parents: 0
diff changeset
3 ultrafast universal RNA-seq aligner
0
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
4 </description>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
5 <requirements>
4
804fe260ee6c planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents: 1
diff changeset
6 <requirement type="package" version="2.5">pandoc</requirement>
804fe260ee6c planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents: 1
diff changeset
7 <requirement type="package" version="1.20.2">r-getopt</requirement>
804fe260ee6c planemo upload commit 841d8b22bf9f1aaed6bfe8344b60617f45b275b2-dirty
mingchen0919
parents: 1
diff changeset
8 <requirement type="package" version="1.10">r-rmarkdown</requirement>
0
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
9 <requirement type="package" version="2.5.4a">star</requirement>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
10 <requirement type="package" version="1.7">samtools</requirement>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
11 </requirements>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
12 <command><![CDATA[
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
13
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
14 ######### each aurora tool generates a html file and have an files path directory associated with it.
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
15 mkdir -p $report.files_path &&
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
16
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
17 ######### three important paths:
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
18 ######### 1. path to tool installation directory
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
19 ######### 2. path to report html
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
20 ######### 3. path to files_path directory associated with the report output.
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
21 export TOOL_INSTALL_DIR='${__tool_directory__}' &&
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
22 export REPORT='$report' &&
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
23 export REPORT_FILES_PATH='$report.files_path' &&
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
24
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
25 ############ create a hidden file to store r markdown rendering log
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
26 touch $report.files_path/.r_rendering.log.txt &&
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
27
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
28 ############ finally run the render.R script
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
29 Rscript '${__tool_directory__}/rmarkdown_report_render.R'
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
30
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
31 -o $report
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
32 -d $report.files_path
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
33
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
34 -A '$genomeFastaFiles'
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
35 -B '$sjdbGTFfile'
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
36 -C '$sjdbOverhang'
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
37 -F '$first_reads'
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
38 -R '$second_reads'
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
39 -S '$sorted_bam'
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
40
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
41 ]]></command>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
42 <inputs>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
43 <param type="data" name="first_reads" label="First reads" optional="False" format="fastq,fastqsanger"/>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
44 <param type="data" name="second_reads" label="Second reads" optional="True" format="fastq,fastqsanger"/>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
45 <param type="data" name="genomeFastaFiles" argument="--genomeFastaFiles" label="Genome fasta files"
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
46 optional="False" format="fasta,fa"/>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
47 <param type="data" name="sjdbGTFfile" argument="--sjdbGTFfile" label="Annotated transcripts"
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
48 help="the file with annotated transcripts in the standard GTF format. STAR will extract splice junctions from this file and use them to greatly improve accuracy of the mapping. While this is optional, and STAR can be run without annotations, using annotations is highly recommended whenever they are available."
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
49 optional="True" format="gtf"/>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
50 <param type="integer" name="sjdbOverhang" argument="--sjdbOverhang" label="sjdbOverhang"
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
51 help="the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database. Ideally, this length should be equal to the ReadLength-1, where ReadLength is the length of the reads. For instance, for Illumina 2x100b paired-end reads, the ideal value is 100-1=99. In case of reads of varying length, the ideal value is max(ReadLength)-1. In most cases, a generic value of 100 will work as well as the ideal value."
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
52 optional="False" value="100" min="1"/>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
53 </inputs>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
54 <outputs>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
55 <data name="report" format="html" label="${tool.name} report on ${on_string}"/>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
56 <data name="sorted_bam" format="bam" label="${tool.name} sorted bam on ${on_string}"/>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
57 </outputs>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
58 <citations>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
59 <citation type="bibtex"><![CDATA[
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
60 @article{allaire2016rmarkdown,
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
61 title={rmarkdown: Dynamic Documents for R, 2016},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
62 author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
63 and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
64 journal={R package version 0.9},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
65 volume={6},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
66 year={2016}
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
67 }
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
68 ]]></citation>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
69 <citation type="bibtex"><![CDATA[
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
70 @book{xie2015dynamic,
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
71 title={Dynamic Documents with R and knitr},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
72 author={Xie, Yihui},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
73 volume={29},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
74 year={2015},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
75 publisher={CRC Press}
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
76 }
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
77 ]]></citation>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
78 <citation type="bibtex"><![CDATA[
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
79 @online{jstree,
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
80 author={Bozhanov, Ivan},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
81 year = 2018,
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
82 url = {https://www.jstree.com/}
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
83 }
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
84 ]]></citation>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
85 <citation type="bibtex"><![CDATA[
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
86 @article{dobin2013star,
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
87 title={STAR: ultrafast universal RNA-seq aligner},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
88 author={Dobin, Alexander and Davis, Carrie A and Schlesinger, Felix and Drenkow, Jorg and Zaleski, Chris and Jha, Sonali and Batut, Philippe and Chaisson, Mark and Gingeras, Thomas R},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
89 journal={Bioinformatics},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
90 volume={29},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
91 number={1},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
92 pages={15--21},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
93 year={2013},
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
94 publisher={Oxford University Press}
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
95 }
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
96 ]]></citation>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
97 </citations>
c12e291895ff planemo upload commit 104ae24ee30761a0099eeb91362ed1e3e13aba4b
mingchen0919
parents:
diff changeset
98 </tool>