| Next changeset 1:b9b2da3fa7d7 (2015-02-10) |
|
Commit message:
Uploaded |
|
added:
fastaptamer_count_1.xml |
| b |
| diff -r 000000000000 -r 2bed8ca187a1 fastaptamer_count_1.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastaptamer_count_1.xml Tue Feb 10 14:22:39 2015 -0500 |
| b |
| @@ -0,0 +1,59 @@ +<tool id="fastaptamer_count_1_0_2" name="FASTAptamer-Count" version="1.0.2"> + + <description>Count, rank, sort and normalize sequence reads in a selection population.</description> + + <version_command>fastaptamer_count -v</version_command> + + <command interpreter="perl">fastaptamer_count -i $input -o $output</command> + + <inputs> + <param name="input" type="data" format="fastq" label="Input file" help="Must be FASTQ and should be pre-processed (filtered for quality and trimmed of constant regions)."></param> + </inputs> + + <outputs> + <data name="output" format="fasta" label="FASTAptamer-Count output file"></data> + </outputs> + + <help> + +.. class:: warningmark + +FASTAptamer-Count requires FASTQ formatted input files. + +.. class:: infomark + +Input files should be trimmed of constant regions and filtered for only high-quality reads. + +------ + +**FASTAptamer-Count** serves as the gateway to the FASTAptamer suite of bioinformatics tools for combinatorial selections. + +For a given FASTQ input file, FASTAptamer-Count will determine the number of times each sequence was read, normalize sequence frequency to reads per million, and rank and sort sequences by decreasing total reads. + +Output is generated as a sorted and non-redundant FASTA formatted file in which each unique sequence generates a FASTA entry with the following information in the description line: + + >RANK-READS-RPM + +RANK is the relative abundance of the sequence within the population. In cases where two or more sequences are sampled with equal abundance, FASTAptamer-Count follows standard competition ranking (e.g., “1-2-2-4” where two sequences are tied for second). READS is the raw number of times a sequence was counted. RPM is “Reads per million,” which is a normalized value that allows for comparison across populations of varying read depth. RPM is calculated as: RPM = (READS/(population size)) x 10^6. + +------ + +.. image:: + http://burkelab.missouri.edu/images/fastaptamer-logo-xs.png + :height: 98 + :width: 300 + +For more information on FASTAptamer, visit our website_. + +FASTAptamer is distributed under a GNU GPL v3.0 license. For complete license click here_. + +.. _here: http://burkelab.missouri.edu/fastaptamer/LICENSE.txt +.. _website: http://burkelab.missouri.edu/fastaptamer.html + + </help> + + <citations> + <citation type="doi">doi:10.1038/mtna.2015.4</citation> + </citations> + +</tool> |