Mercurial > repos > mingchen0919 > rmarkdown_bdss_client

annotate bdss_client_sra_se.xml @ 7:efb1938c3020 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_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
author mingchen0919
date Wed, 11 Oct 2017 13:21:54 -0400
parents 04100e773314
children afecbcdaba60
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
1 <tool id="rmarkdown_bdss_client_sra_se" name="BDSS client SRA SE" version="1.0.0">
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
2 <requirements>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
3 <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
4 <requirement type="package" version="1.20.0">r-getopt</requirement>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
5 <requirement type="package" version="1.2">r-rmarkdown</requirement>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
6 <requirement type="package" version="0.3.5">r-htmltools</requirement>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
7 <requirement type="package" version="0.5.0">r-dplyr</requirement>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
8 <requirement type="package" version="0.5.4">parallel-fastq-dump</requirement>
3
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 1
diff changeset
9 <requirement type="package" version="1.95_4.8">r-rcurl</requirement>
0
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
10 </requirements>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
11 <description>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
12 Download and extract single end reads in fastq or fasta format from NCBI SRA. The output is a list of datasets
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
13 collection.
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
14 </description>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
15 <stdio>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
16 <!--All stderr are redirected to a file. "XXX" is used to match with nothing-->
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
17 <regex match="XXX"
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
18 source="stderr"
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
19 level="warning"
3
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 1
diff changeset
20 description="Check the warnings_and_errors.txt file for more details."/>
0
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
21 </stdio>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
22 <command>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
23 <![CDATA[
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
24 Rscript '${__tool_directory__}/bdss_client_sra_se_render.R'
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
25 -i '$sra_accession'
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
26 -e $echo
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
27 -f $format
3
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 1
diff changeset
28 -S $sra
0
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
29
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
30 -r $report
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
31 -d $report.files_path
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
32 -s $sink_message
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
33
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
34 -t '${__tool_directory__}/bdss_client_sra_se.Rmd'
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
35 ]]>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
36 </command>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
37 <inputs>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
38 <param type="text" name="sra_accession" label="SRR/DRR/ERR accessions"
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
39 help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/>
3
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 1
diff changeset
40 <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true"
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 1
diff changeset
41 label="output files in fastq (Yes) or fasta (No)?"/>
5
04100e773314 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 3
diff changeset
42 <param type="boolean" name="sra" truevalue="TRUE" falsevalue="FALSE" checked="true"
3
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 1
diff changeset
43 label="Download SRA or Fastq"/>
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 1
diff changeset
44 <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false"
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 1
diff changeset
45 label="Display analysis code in report?"/>
0
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
46 </inputs>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
47 <outputs>
3
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 1
diff changeset
48 <data format="html" name="report" label="BDSS report"/>
1
d9aeb2e7c53d planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents: 0
diff changeset
49 <collection type="list" name="list_collection" label="BDSS fastq/fasta (single end reads)">
3
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 1
diff changeset
50 <discover_datasets pattern="__name_and_ext__" directory="read_files_directory"/>
0
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
51 </collection>
3
c707a4178832 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit ea6df97960569d247d64be1549aa90768c9786f4-dirty
mingchen0919
parents: 1
diff changeset
52 <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/>
0
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
53 </outputs>
614e9553f366 planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 36de2ee9751d1ef5db0c76c217fd5ba262ca3739-dirty
mingchen0919
parents:
diff changeset
54 </tool>