Mercurial > repos > tyty > structurefold
changeset 88:40b8071a44f7 draft
Deleted selected files
| author | tyty |
|---|---|
| date | Fri, 19 Dec 2014 13:58:26 -0500 |
| parents | 5a9183ec344f |
| children | 361dc1047dc0 |
| files | get_reads/get_read.xml |
| diffstat | 1 files changed, 0 insertions(+), 46 deletions(-) [+] |
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--- a/get_reads/get_read.xml Fri Dec 19 13:23:03 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -<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>