# HG changeset patch # User Matt Shirley # Date 1371663118 14400 # Node ID d850324e82cf03a60431de095bc4bd3827dc24e8 # Parent a1255154fa3f96f504e2abfa5e25b4398b407301 fix datatype reference, increment versions diff -r a1255154fa3f -r d850324e82cf fastq_dump.xml --- a/fastq_dump.xml Mon Jun 17 21:41:27 2013 -0400 +++ b/fastq_dump.xml Wed Jun 19 13:31:58 2013 -0400 @@ -1,9 +1,9 @@ - + format reads from NCBI SRA. fastq-dump --log-level fatal --accession '${input.name}' --stdout $split $aligned '$input' > $output fastq-dump --version - + diff -r a1255154fa3f -r d850324e82cf sam_dump.xml --- a/sam_dump.xml Mon Jun 17 21:41:27 2013 -0400 +++ b/sam_dump.xml Wed Jun 19 13:31:58 2013 -0400 @@ -1,9 +1,9 @@ - + format reads from NCBI SRA. sam-dump $header $aligned $primary '$input' > $output sam-dump --version - + @@ -27,7 +27,8 @@ sra_toolkit - This tool extracts SAM format reads from SRA archives using sam-dump. The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. -Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. + This tool extracts SAM format reads from SRA archives using sam-dump. + The sam-dump program is developed at NCBI, and is available at: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. + Contact Matt Shirley at mdshw5@gmail.com for support and bug reports. diff -r a1255154fa3f -r d850324e82cf sra_fetch.xml --- a/sra_fetch.xml Mon Jun 17 21:41:27 2013 -0400 +++ b/sra_fetch.xml Wed Jun 19 13:31:58 2013 -0400 @@ -1,4 +1,4 @@ - + by accession from NCBI SRA. sra_fetch.py --accession '$accession' --out '$output' @@ -7,9 +7,6 @@ - - sra_fetch.py - This tool fetches SRA archives from NCBI over FTP using the python ftplib.