Mercurial > repos > mingchen0919 > rmarkdown_mirdeep2

annotate mirdeep2_mapper.xml @ 4:543ee6fdadeb draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
author mingchen0919
date Tue, 08 Aug 2017 15:06:46 -0400
parents 228117ad62bb
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
1 <tool id="mirdeep2_mapper_site" name="mirdeep2_mapper" version="1.0.0">
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
2 <requirements>
4
543ee6fdadeb planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
mingchen0919
parents: 3
diff changeset
3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
0
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
4 <requirement type="package" version="2.0.0.8">mirdeep2</requirement>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
5 <requirement type="package" version="1.20.0">r-getopt</requirement>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
6 <requirement type="package" version="1.2">r-rmarkdown</requirement>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
7 <requirement type="package" version="1.8.4">r-plyr</requirement>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
8 <requirement type="package" version="0.5.0">r-dplyr</requirement>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
9 <requirement type="package" version="0.3.5">r-htmltools</requirement>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
10 </requirements>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
11 <description>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
12 Mapping reads to genome
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
13 </description>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
14 <stdio>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
15 <regex match="Execution halted"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
16 source="both"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
17 level="fatal"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
18 description="Execution halted." />
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
19 <regex match="Error in"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
20 source="both"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
21 level="fatal"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
22 description="An undefined error occured, please check your intput carefully and contact your administrator." />
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
23 <regex match="Fatal error"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
24 source="both"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
25 level="fatal"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
26 description="An undefined error occured, please check your intput carefully and contact your administrator." />
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
27 </stdio>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
28 <command>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
29 <![CDATA[
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
30
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
31 Rscript '${__tool_directory__}/mirdeep2_mapper_render.R'
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
32
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
33 ## 1. input data
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
34 -r $reads
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
35 -g $reference_genome
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
36 -e $echo
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
37
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
38 ## 2. output report and report site directory
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
39 -o $mirdeep2_mapper_site
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
40 -d $mirdeep2_mapper_site.files_path
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
41 -m $reads_collapsed
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
42 -n $reads_collapsed_vs_genome
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
43 -t $report_log
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
44
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
45 ## other parameters
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
46 -b $parse_to_fasta
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
47 -c $clean_entries
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
48 -f $clip_3_adapter
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
49 -h $discard_shorter_reads
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
50 -j $collapse_reads_or_not
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
51 -k $map_with_one_mismatch
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
52 -l $map_up_to_position
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
53
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
54
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
55 ## 3. Rmd templates sitting in the tool directory
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
56
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
57 ## other Rmd body template files
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
58 -p '${__tool_directory__}/mirdeep2_mapper.Rmd'
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
59
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
60
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
61
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
62 ]]>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
63 </command>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
64 <inputs>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
65 <param name="reads" type="data" format="fastq,fasta" multiple="False" optional="False"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
66 label="Read input file" help="Reads in fastq or fasta format"/>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
67 <param name="reference_genome" type="data" format="fasta" multiple="false" optional="False" argument="-p"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
68 label="Reference genome from history" />
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
69
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
70 <param name="parse_to_fasta" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-h"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
71 optional="True" label="Parse to fasta format" />
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
72 <param name="clean_entries" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-j"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
73 optional="True" label="Remove reads with non-canonical letters"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
74 help="remove all entries that have a sequence that contains letters other than a,c,g,t,u,n,A,C,G,T,U,N" />
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
75 <param name="clip_3_adapter" type="text" argument="-k" value="" optional="true" label="Clip 3' adapter sequence (optional)"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
76 help="Enter an adapter sequence"/>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
77 <param name="discard_shorter_reads" type="integer" min="0" value="18" argument="-l"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
78 label="Discard reads shorter than int nts" />
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
79 <param name="collapse_reads_or_not" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="true" argument="-m"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
80 label="Collapse reads" />
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
81 <param name="map_with_one_mismatch" type="boolean" truevalue="TRUE" falsevalue="FALSE" argument="-q"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
82 label="Map with one mismatch"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
83 help="map with one mismatch in the seed (mapping takes longer)"/>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
84 <param name="map_up_to_position" type="integer" min="1" value="5" label="Map up to int nts" argument="-r"
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
85 help="A read is allowed to map up to this number of positions in the genome. Default is 5"/>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
86
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
87 <param name="echo" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
88 </inputs>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
89 <outputs>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
90 <data name="mirdeep2_mapper_site" format="html" label="mirdeep2_mapper site" />
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
91 <data name="reads_collapsed" format="fasta" label="reads_collapsed" />
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
92 <data name="reads_collapsed_vs_genome" format="tabular" label="reads_collapsed_vs_ref_genome" />
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
93 <data name="report_log" format="txt" label="report log"/>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
94 </outputs>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
95 <citations>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
96 @article{friedlander2011mirdeep2,
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
97 title={miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
98 author={Friedl{\"a}nder, Marc R and Mackowiak, Sebastian D and Li, Na and Chen, Wei and Rajewsky, Nikolaus},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
99 journal={Nucleic acids research},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
100 volume={40},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
101 number={1},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
102 pages={37--52},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
103 year={2011},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
104 publisher={Oxford University Press}
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
105 }
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
106 <citation type="bibtex">
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
107 @article{allaire2016rmarkdown,
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
108 title={rmarkdown: Dynamic Documents for R, 2016},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
109 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},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
110 journal={R package version 0.9},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
111 volume={6},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
112 year={2016}
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
113 }
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
114 </citation>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
115 <citation type="bibtex">
2
90207652b06a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
116 @article{allaire2016rmarkdown,
90207652b06a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
117 title={rmarkdown: Dynamic Documents for R, 2016},
90207652b06a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
118 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},
90207652b06a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
119 journal={R package version 0.9},
90207652b06a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
120 volume={6},
90207652b06a planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
121 year={2016}
0
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
122 }
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
123 </citation>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
124 <citation type="bibtex">
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
125 @book{xie2015dynamic,
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
126 title={Dynamic Documents with R and knitr},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
127 author={Xie, Yihui},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
128 volume={29},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
129 year={2015},
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
130 publisher={CRC Press}
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
131 }
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
132 </citation>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
133 </citations>
963905bcb754 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_mirdeep2 commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents:
diff changeset
134 </tool>