comparison get_reads/get_read.xml~ @ 25:90bc1ead3abd draft

Uploaded
author tyty
date Mon, 20 Oct 2014 14:41:41 -0400
parents
children
comparison
equal deleted inserted replaced
24:fcc92680e802 25:90bc1ead3abd
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="0.1.18">samtools</requirement>
7 </requirements>
8 <inputs>
9 <param name="lib_file" type="data" format="fasta" label="Library file (fasta)"/>
10 <param name="map_file" type="data" format="bam" label="Mapped file"/>
11 </inputs>
12 <outputs>
13 <data name="output" format="txt"/>
14 </outputs>
15 <tests>
16 <test>
17 <param name="lib_file" value="test.bam" />
18 <param name="map_file" value="com_rna.txt" />
19 <output name="output" file="get_RT_stop_test.out" />
20
21 </test>
22 </tests>
23
24 <help>
25
26
27 **TIPS**:
28
29 -----
30
31 **Input**
32 1. A mapped (bam) file from Bowtie (or any mapping program)
33 2. Reference library sequences (fasta) used to map the reads
34
35 -----
36
37 **Output**:
38 A text file with reverse transcription stop counts mapped to each nucleotide (RTSC file)
39
40
41
42 </help>
43 </tool>