Mercurial > repos > tyty > structurefold
diff get_reads/get_read.xml @ 50:6747060cdfe6 draft
Uploaded
author | tyty |
---|---|
date | Mon, 27 Oct 2014 01:50:00 -0400 |
parents | |
children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/get_reads/get_read.xml Mon Oct 27 01:50:00 2014 -0400 @@ -0,0 +1,44 @@ +<tool id="get_read_pipeline" name="Get RT Stop Counts" version="1.0"> + <description></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> + + +**TIPS**: + +----- + +**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>