Mercurial > repos > mingchen0919 > rmarkdown_i_adhore

annotate i-adhore.xml @ 7:f86be5aeea36 draft

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_i_adhore commit cc2f473d151c0de971c760a9aec9d09ff073ad85-dirty
author mingchen0919
date Fri, 25 Aug 2017 12:04:15 -0400
parents 85166d75910b
children f8bedb407e5c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
1 <tool id="i_adhore" name="i-adhore" version="0.1">
1
fd719a0a6b26 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 0
diff changeset
2 <requirements>
4
85166d75910b planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit a23e23222252167ef7c3338a4872e84706df8f83-dirty
mingchen0919
parents: 3
diff changeset
3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
1
fd719a0a6b26 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 0
diff changeset
4 <requirement type="package" version="1.20.0">r-getopt</requirement>
fd719a0a6b26 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 0
diff changeset
5 <requirement type="package" version="1.2">r-rmarkdown</requirement>
fd719a0a6b26 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 0
diff changeset
6 <requirement type="package" version="1.8.4">r-plyr</requirement>
fd719a0a6b26 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 0
diff changeset
7 <requirement type="package" version="0.5.0">r-dplyr</requirement>
fd719a0a6b26 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 0
diff changeset
8 </requirements>
0
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
9 <description>Generate i-adhore configure file</description>
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
10 <stdio>
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
11 <exit_code range="1:" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
12 <exit_code range=":-1" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
13 <regex match="Error:" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
14 <regex match="Exception:" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
15 </stdio>
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
16 <command><![CDATA[
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
17
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
18 Rscript '${__tool_directory__}/i_adhore_configure_render.R'
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
19
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
20 ## 1. input data
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
21 -e $echo
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
22
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
23 #set $g_analysis_files = ''
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
24 #for $g in $genomes
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
25 #if str($g.genome_name)
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
26 #set $analysis_files = []
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
27 #for $file in $g.analysis_files.to_dataset_instances($g.analysis_files)
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
28 #set $analysis_files += [$file.__str__]
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
29 #end for
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
30 #set g_analysis_files += str($g.genome_name) + ':' + ','.join($analysis_files) + ';'
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
31 #end if
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
32 #end for
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
33 -G '$g_analysis_files'
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
34
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
35 -b $blast_table
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
36 -g $gap_size
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
37 -c $cluster_gap
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
38 -q $q_value
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
39 -p $prob_cutoff
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
40 -a $anchor_points
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
41 -m $alignment_method
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
42 -l $level2only
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
43 -T $table_type
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
44 -h $multi_hypothesis_correction
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
45
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
46 ## 2. output report and file directory
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
47 -x $i_adhore_configure_txt
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
48 -o $i_adhore_configure
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
49 -d $i_adhore_configure.files_path
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
50
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
51 ## 3. Rmd templates in the tool directory
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
52 -t '${__tool_directory__}/i_adhore_configure.Rmd'
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
53
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
54
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
55 ]]></command>
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
56 <inputs>
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
57 <repeat name="genomes" title="genome" min="1">
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
58 <param name="genome_name" type="text" value="" label="Specify genome name" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
59 <param name="analysis_files" type="data" format="txt" multiple="true" label="analysis files (.lst or .txt files)" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
60 </repeat>
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
61 <param name="blast_table" type="data" format="csv" multiple="false" label="blast table (.csv file)" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
62 <param name="gap_size" type="text" value="30" label="gap size" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
63 <param name="cluster_gap" type="text" value="35" label="cluster gap" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
64 <param name="q_value" type="text" value="0.75" label="q value" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
65 <param name="prob_cutoff" type="text" value="0.01" label="probability cutoff" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
66 <param name="anchor_points" type="text" value="3" label="anchor_points" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
67 <param name="alignment_method" type="text" value="gg4" label="alignment method" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
68 <param name="level2only" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="level 2 only" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
69 <param name="table_type" type="text" value="family" label="table type" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
70 <param name="multi_hypothesis_correction" type="text" value="FDR" label="multiple hypothesis correction" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
71
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
72 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
73 </inputs>
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
74 <outputs>
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
75 <data name="i_adhore_configure" format="html" label="i-adhore configure report" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
76 <data name="i_adhore_configure_txt" format="txt" label="i-adhore configure file" />
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
77 </outputs>
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
78 <citations>
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
79 <citation type="bibtex">
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
80 @article{allaire2016rmarkdown,
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
81 title={rmarkdown: Dynamic Documents for R, 2016},
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
82 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},
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
83 journal={R package version 0.9},
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
84 volume={6},
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
85 year={2016}
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
86 }
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
87 </citation>
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
88 <citation type="bibtex">
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
89 @book{xie2015dynamic,
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
90 title={Dynamic Documents with R and knitr},
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
91 author={Xie, Yihui},
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
92 volume={29},
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
93 year={2015},
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
94 publisher={CRC Press}
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
95 }
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
96 </citation>
2
dca9b0c49c0e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
97 <citation type="bibtex">
dca9b0c49c0e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
98 @book{xie2015dynamic,
dca9b0c49c0e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
99 title={Dynamic Documents with R and knitr},
dca9b0c49c0e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
100 author={Xie, Yihui},
dca9b0c49c0e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
101 volume={29},
dca9b0c49c0e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
102 year={2015},
dca9b0c49c0e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
103 publisher={CRC Press}
dca9b0c49c0e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
104 }
dca9b0c49c0e planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit 29e8b40899c71ca12fd07b2bb530b0ee65037588-dirty
mingchen0919
parents: 1
diff changeset
105 </citation>
0
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
106 </citations>
9755ce6ac4d5 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_i_adhore commit b6ef011f29d6c75775be9cc0e0abe53e19981d1d-dirty
mingchen0919
parents:
diff changeset
107 </tool>