Mercurial > repos > peterjc > fastq_pair_names
changeset 9:9e0212695094 draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/fastq_pair_names commit 3ab3d1a9650dec0533344d710ceb027e482d2b10-dirty
| author | peterjc |
|---|---|
| date | Fri, 09 Nov 2018 10:52:02 -0500 |
| parents | 0ffb956f0a6b |
| children | 8ceccb6738de |
| files | tools/fastq_pair_names/fastq_pair_names.py tools/fastq_pair_names/fastq_pair_names.xml |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/tools/fastq_pair_names/fastq_pair_names.py Fri Sep 15 10:23:49 2017 -0400 +++ b/tools/fastq_pair_names/fastq_pair_names.py Fri Nov 09 10:52:02 2018 -0500 @@ -2,7 +2,7 @@ """Extract paired read names from FASTQ file(s). The input file should be a valid FASTQ file(s), the output is two tabular -files - the paired read names (without suffices), and unpaired read names +files - the paired read names (without suffixes), and unpaired read names (including any unrecognised pair names). Note that the FASTQ variant is unimportant (Sanger, Solexa, Illumina, or even
--- a/tools/fastq_pair_names/fastq_pair_names.xml Fri Sep 15 10:23:49 2017 -0400 +++ b/tools/fastq_pair_names/fastq_pair_names.xml Fri Nov 09 10:52:02 2018 -0500 @@ -1,5 +1,5 @@ <tool id="fastq_pair_names" name="Identify paired reads in FASTQ files" version="0.0.5"> - <description>using the read name suffices</description> + <description>using the read name suffixes</description> <requirements> <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> </requirements> @@ -34,7 +34,7 @@ The input file should be a valid FASTQ file which has been sorted so that any partner forward+reverse reads are consecutive. The output files all preserve this sort order. Pairing are recognised based on standard name -suffices (see below). +suffixes (see below). Any reads where the forward/reverse naming suffix used is not recognised are treated as orphan reads. The tool supports the /1 and /2 convention @@ -75,7 +75,7 @@ Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PeerJ 1:e167 -http://dx.doi.org/10.7717/peerj.167 +https://doi.org/10.7717/peerj.167 This tool is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/fastq_pair_names