Mercurial > repos > mingchen0919 > rmarkdown_bdss_client
changeset 23:fd15cf620d5d draft
planemo upload for repository https://github.com/statonlab/docker-GRReport/tree/master/my_tools/rmarkdown_bdss_client commit 3d2a2c46f10b7f00a36771d2a0fc334d2c177730-dirty
| author | mingchen0919 |
|---|---|
| date | Sun, 15 Oct 2017 00:50:10 -0400 |
| parents | 89cc5b026494 |
| children | a1c0ebd05f2f |
| files | bdss_client.Rmd bdss_client_sra.Rmd bdss_client_sra.xml |
| diffstat | 3 files changed, 17 insertions(+), 12 deletions(-) [+] |
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--- a/bdss_client.Rmd Sat Oct 14 22:59:06 2017 -0400 +++ b/bdss_client.Rmd Sun Oct 15 00:50:10 2017 -0400 @@ -41,7 +41,7 @@ # loop through SRA accessions to download and extract reads. for(url in urls) { print(url) - bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer --destination read_files_directory -u ', url) + bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer --destination read_files_directory -u ', url) print(bdss_command) print(system(bdss_command, intern = TRUE)) }
--- a/bdss_client_sra.Rmd Sat Oct 14 22:59:06 2017 -0400 +++ b/bdss_client_sra.Rmd Sun Oct 15 00:50:10 2017 -0400 @@ -46,7 +46,7 @@ substr(id, 1, 3), '/', substr(id, 1, 6), '/', id, '/', id, '.sra') # download sra file with bdss - bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url) + bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url) system(bdss_command, intern = TRUE) # convert .sra to .fastq/.fasta if('FORMAT' == 'fasta') { @@ -68,7 +68,7 @@ substr(id, 1, 3), '/', substr(id, 1, 6), '/', id, '/', id, '.sra') # download sra file with bdss - bdss_command = paste0('/tool_deps/_conda/bin/bdss transfer -u ', url) + bdss_command = paste0('/main/sites/galaxy/galaxy/tools/_conda/bin/bdss transfer -u ', url) system(bdss_command, intern = TRUE) # convert .sra to .fastq/.fasta if('FORMAT' == 'fasta') { @@ -79,9 +79,9 @@ cat('----convert SRA to fastq/fasta------\n') command_stdout = system(command, intern = TRUE) print(command_stdout) - if(length(command_stdout) < 3) { + if(!(paste0(id, '_2.FORMAT') %in% list.files('pe_read_files_directory'))) { # this is not a paired end SRA file. The corresponding file will be deleted. - cat(paste0(id, 'is not paired end SRA, the corresponding fastq/fasta file will deleted.')) + cat(paste0(id, ' is not paired end SRA, the corresponding fastq/fasta file will deleted.')) system(paste0('rm pe_read_files_directory/', id, '_1.*'), intern = TRUE) } @@ -95,8 +95,10 @@ cat('-----Renaming files------\n') # rename files for paired end reads old_files = paste0('./pe_read_files_directory/', list.files('./pe_read_files_directory')) +print(old_files) new_files = gsub('_1', '_forward', old_files) new_files = gsub('_2', '_reverse', new_files) +print(new_files) file.rename(old_files, new_files) ```
--- a/bdss_client_sra.xml Sat Oct 14 22:59:06 2017 -0400 +++ b/bdss_client_sra.xml Sun Oct 15 00:50:10 2017 -0400 @@ -10,7 +10,8 @@ <requirement type="package" version="1.95_4.8">r-rcurl</requirement> </requirements> <description> - Download data with BDSS client and generate list (single end SRA data) and list:paired dataset collection (paired end SRA data). + Download data with BDSS client and generate list (single end SRA data) and list:paired dataset collection + (paired end SRA data). </description> <stdio> <!--All stderr are redirected to a file. "XXX" is used to match with nothing--> @@ -35,10 +36,10 @@ ]]> </command> <inputs> - <param type="text" name="sra_ids_se" area="true" size="5x25" label="SRR/DRR/ERR accessions of single end SRA" optional="false" - help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR6077558,ERR343809"/> - <param type="text" name="sra_ids_pe" area="true" size="5x25" label="SRR/DRR/ERR accessions of paired end SRA" optional="false" - help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. ERR2105526"/> + <param type="text" name="sra_ids_se" area="true" size="5x25" label="SRR/DRR/ERR accessions of single end SRA" + help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. SRR039885"/> + <param type="text" name="sra_ids_pe" area="true" size="5x25" label="SRR/DRR/ERR accessions of paired end SRA" + help="A list of SRR/DRR/ERR accessions separated by comma or space. e.g. ERR1679739"/> <param type="boolean" name="format" truevalue="fastq" falsevalue="fasta" checked="true" label="output files in fastq (Yes) or fasta (No)?"/> <param type="boolean" name="echo" truevalue="TRUE" falsevalue="FALSE" checked="false" @@ -48,11 +49,13 @@ <data format="html" name="report" label="BDSS client report"/> <!--list dataset collection for single end SRA data--> <collection type="list" name="list_collection" label="BDSS download data (single end reads)"> - <discover_datasets pattern="__name_and_ext__" directory="se_read_files_directory" /> + <discover_datasets pattern="__name_and_ext__" directory="se_read_files_directory"/> </collection> <!--list:paired dataset collection for paired end SRA data--> <collection type="list:paired" name="list:paired_collection" label="BDSS download data (paired end reads)"> - <discover_datasets pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.(?P<ext>[^\._]+)?" directory="pe_read_files_directory" /> + <discover_datasets + pattern="(?P<identifier_0>[^_]+)_(?P<identifier_1>[^_]+)\.(?P<ext>[^\._]+)?" + directory="pe_read_files_directory"/> </collection> <data format="txt" name="sink_message" label="Warnings and Errors" from_work_dir="warnings_and_errors.txt"/> </outputs>