Mercurial > repos > tyty > structurefold
comparison get_reads/get_read.xml @ 7:b10c6790f01e draft
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author | tyty |
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date | Mon, 15 Sep 2014 14:55:21 -0400 |
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6:1a909794e94d | 7:b10c6790f01e |
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1 <tool id="get_read_pipeline" name="Get RT stop counts" version="1.0"> | |
2 <description></description> | |
3 <command interpreter="python">get_read.py $lib_file $map_file $output </command> | |
4 <requirements> | |
5 <requirement type="package" version="1.61">biopython</requirement> | |
6 <requirement type="package" version="1.7">numpy</requirement> | |
7 <requirement type="package" version="0.1.18">samtools</requirement> | |
8 </requirements> | |
9 <inputs> | |
10 <param name="lib_file" type="data" format="fasta" label="Library file (fasta)"/> | |
11 <param name="map_file" type="data" format="bam" label="Mapped file"/> | |
12 </inputs> | |
13 <outputs> | |
14 <data name="output" format="txt"/> | |
15 </outputs> | |
16 <tests> | |
17 <test> | |
18 <param name="lib_file" value="test.bam" /> | |
19 <param name="map_file" value="com_rna.txt" /> | |
20 <output name="output" file="get_RT_stop_test.out" /> | |
21 | |
22 </test> | |
23 </tests> | |
24 | |
25 <help> | |
26 | |
27 | |
28 **TIPS**: | |
29 | |
30 ----- | |
31 | |
32 **Input** | |
33 1. A mapped (bam) file from Bowtie (or any mapping program) | |
34 2. Reference library sequences (fasta) used to map the reads | |
35 | |
36 ----- | |
37 | |
38 **Output**: | |
39 A text file with reverse transcription stop counts mapped to each nucleotide (RTSC file) | |
40 | |
41 | |
42 | |
43 </help> | |
44 </tool> |