Mercurial > repos > tyty > structurefold
comparison get_reads/get_read.xml @ 85:6b7429975fde draft
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author | tyty |
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date | Fri, 19 Dec 2014 13:22:06 -0500 |
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84:c3092769835e | 85:6b7429975fde |
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1 <tool id="get_read_pipeline" name="Get RT Stop Counts" version="1.0"> | |
2 <description>derives the reverse transcriptase (RT) stop count on each nucleotide from a mapped file provided by the Iterative Mapping module</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="1.7.1">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="Reference genome/transcriptome"/> | |
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 **Function** | |
27 | |
28 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. | |
29 | |
30 ----- | |
31 | |
32 **Input**: | |
33 | |
34 * 1. A mapped (.bam) file from Bowtie (or any other mapping program) | |
35 * 2. Reference library sequences (fasta) used to map the reads to | |
36 | |
37 ----- | |
38 | |
39 **Output**: | |
40 | |
41 A text file with reverse transcription stop counts mapped to each nucleotide (RTSC file) | |
42 | |
43 | |
44 | |
45 </help> | |
46 </tool> |