Mercurial > repos > lxue > ageseq
changeset 4:32c73c20f12f draft
Deleted selected files
| author | lxue |
|---|---|
| date | Fri, 15 May 2015 16:43:19 -0400 |
| parents | af338b471ed3 |
| children | 6f05e59194b9 |
| files | AGEseq.xml |
| diffstat | 1 files changed, 0 insertions(+), 38 deletions(-) [+] |
line wrap: on
line diff
--- a/AGEseq.xml Fri May 15 16:40:48 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,38 +0,0 @@ -<tool id="AGEseq" name="AGEseq"> - <description>Analysis of Genome Editing by Sequencing</description> - <command interpreter="perl">AGEseq_web.pl $target $read $mismatch $minAbundance $wtNum $indelNum $output </command> - <inputs> - <param format="txt" name="target" type="data" label="Target File (Reference Table)" help="Select target/reference file."/> - <param format="" name="read" type="data" label="Read file (Sanger or NGS)" help="Select read file in fasta or fastq format." /> - - - <param name="mismatch" type="float" value="0.1" label="Mismatch Rate Cutoff" help="Mismatch rate to filter low quality alignment, default 0.1 (10 %)" /> - <param name="minAbundance" type="integer" value="0" label="Abundance Cutoff" help="Cutoff to filter reads with low abundance, default 0" /> - <param name="wtNum" type="integer" value="20" label="Numbers of WT-like records to be reported" help="Report top xx WT like records, default 20" /> - <param name="indelNum" type="integer" value="50" label="Numbers of records with indel to be reported" help="Report top xx records with indel, default 50" /> - - </inputs> - - <outputs> - <data format="txt" name="output" /> - </outputs> - - - <tests> - <test> - <param name="target" value="targets.txt"/> - <param name="read" value="S2_L001_R1_001.fastq"/> - <output name="out_file1" file="AGEseq_output.txt"/> - </test> - </tests> - - - <help> -**AGEseq** compares amplicon sequences with expected target sequences and finds the insertion/deletion sites in the amplicon sequences. - -Please refer to http://aspendb.uga.edu/downloads or https://github.com/liangjiaoxue/AGEseq for more details. - - - </help> - - </tool> \ No newline at end of file