Mercurial > repos > tyty > structurefold
comparison get_reads/get_read.xml @ 39:c5f80e82efb7 draft
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author | tyty |
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date | Mon, 20 Oct 2014 14:57:26 -0400 |
parents | 90bc1ead3abd |
children | 9fbbe00a2de2 |
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38:b35dc7b728e5 | 39:c5f80e82efb7 |
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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 </test> | |
22 </tests> | |
23 <help> | |
24 | |
25 | |
26 **TIPS**: | |
27 | |
28 ----- | |
29 | |
30 **Input** | |
31 1. A mapped (bam) file from Bowtie (or any mapping program) | |
32 2. Reference library sequences (fasta) used to map the reads | |
33 | |
34 ----- | |
35 | |
36 **Output**: | |
37 A text file with reverse transcription stop counts mapped to each nucleotide (RTSC file) | |
38 | |
39 | |
40 | |
41 </help> | |
42 </tool> |