Mercurial > repos > mingchen0919 > rmarkdown_collection_builder

annotate collection_list_paired.xml @ 6:a0c8b2b25774 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_collection_builder commit 88ca36a41aa577ba888cee39cf81b176bf7e68db
author mingchen0919
date Tue, 26 Sep 2017 13:33:22 -0400
parents 66022ba24ac7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
a0c8b2b25774 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 88ca36a41aa577ba888cee39cf81b176bf7e68db
mingchen0919
parents: 5
diff changeset
1 <tool id="rmarkdown_collection_list_paired" name="Collection type (list:paired)" version="1.0.0">
5
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
2 <requirements>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
4 <requirement type="package" version="1.20.0">r-getopt</requirement>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
5 <requirement type="package" version="1.2">r-rmarkdown</requirement>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
6 <requirement type="package" version="0.3.5">r-htmltools</requirement>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
7 <requirement type="package" version="0.5.0">r-dplyr</requirement>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
8 </requirements>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
9 <description>
6
a0c8b2b25774 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 88ca36a41aa577ba888cee39cf81b176bf7e68db
mingchen0919
parents: 5
diff changeset
10 Create a list of paired dataset collection from files in history.
5
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
11 </description>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
12 <stdio>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
13 <regex match="Execution halted"
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
14 source="both"
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
15 level="fatal"
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
16 description="Execution halted." />
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
17 <regex match="Error in"
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
18 source="both"
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
19 level="fatal"
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
20 description="An undefined error occured, please check your intput carefully and contact your administrator." />
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
21 <regex match="Fatal error"
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
22 source="both"
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
23 level="fatal"
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
24 description="An undefined error occured, please check your intput carefully and contact your administrator." />
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
25 </stdio>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
26 <command>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
27 <![CDATA[
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
28 Rscript '${__tool_directory__}/collection_list_paired_render.R'
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
29 -L $forward_file_list
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
30 -R $reverse_file_list
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
31 -e $echo
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
32 -f $format
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
33
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
34 -r $report
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
35 -d $report.files_path
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
36
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
37 -t '${__tool_directory__}/collection_list_paired.Rmd'
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
38 ]]>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
39 </command>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
40 <inputs>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
41 <param type="data" name="forward_file_list" multiple="true" label="forward inputs"/>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
42 <param type="data" name="reverse_file_list" multiple="true" label="reverse inputs"/>
6
a0c8b2b25774 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 88ca36a41aa577ba888cee39cf81b176bf7e68db
mingchen0919
parents: 5
diff changeset
43 <param type="text" name="format" label="the format (extension) of input files (e.g., fastq, fastqsanger, fasta)"/>
5
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
44
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
45 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Display analysis code in report?" />
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
46 </inputs>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
47 <outputs>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
48 <data format="html" name="report" label="Collection builder (list:paired collection)" />
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
49 <collection type="list:paired" name="list_collection">
6
a0c8b2b25774 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 88ca36a41aa577ba888cee39cf81b176bf7e68db
mingchen0919
parents: 5
diff changeset
50 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.(?P&lt;ext&gt;[^\._]+)?" directory="files_directory"/>
5
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
51 </collection>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
52 </outputs>
66022ba24ac7 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_collection_builder commit 51c9df9f3f883537269f8928f92052457b29f744-dirty
mingchen0919
parents:
diff changeset
53 </tool>