Mercurial > repos > tyty > structurefold
changeset 85:6b7429975fde draft
Uploaded
| author | tyty |
|---|---|
| date | Fri, 19 Dec 2014 13:22:06 -0500 |
| parents | c3092769835e |
| children | e581e89e3318 |
| files | get_reads/get_read.xml |
| diffstat | 1 files changed, 46 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_reads/get_read.xml Fri Dec 19 13:22:06 2014 -0500 @@ -0,0 +1,46 @@ +<tool id="get_read_pipeline" name="Get RT Stop Counts" version="1.0"> + <description>derives the reverse transcriptase (RT) stop count on each nucleotide from a mapped file provided by the Iterative Mapping module</description> + <command interpreter="python">get_read.py $lib_file $map_file $output </command> + <requirements> + <requirement type="package" version="1.61">biopython</requirement> + <requirement type="package" version="1.7.1">numpy</requirement> + <requirement type="package" version="0.1.18">samtools</requirement> + </requirements> + <inputs> + <param name="lib_file" type="data" format="fasta" label="Reference genome/transcriptome"/> + <param name="map_file" type="data" format="bam" label="Mapped file"/> + </inputs> + <outputs> + <data name="output" format="txt"/> + </outputs> + <tests> + <test> + <param name="lib_file" value="test.bam" /> + <param name="map_file" value="com_rna.txt" /> + <output name="output" file="get_RT_stop_test.out" /> + </test> + </tests> + <help> + + +**Function** + +derives the RT stop counts on each nucleotide of each transcript in the reference transcriptome based on a mapped file (.bam), typically the output from the Iterative Mapping module. + +----- + +**Input**: + +* 1. A mapped (.bam) file from Bowtie (or any other mapping program) +* 2. Reference library sequences (fasta) used to map the reads to + +----- + +**Output**: + +A text file with reverse transcription stop counts mapped to each nucleotide (RTSC file) + + + + </help> +</tool>