|
0
|
1 <tool id="RemoveSNPs" name="Remove Mismatches (SNPs) from SAM Alignment file" version="0.1.0">
|
|
|
2 <requirements>
|
|
|
3 </requirements>
|
|
|
4 <command detect_errors="exit_code"><![CDATA[
|
|
|
5 bash $__tool_directory__/RemoveSNPs "$input1" 3 > "$output1"
|
|
|
6 ]]></command>
|
|
|
7 <inputs>
|
|
|
8 <param type="data" name="input1" format="sam" />
|
|
|
9 <param type="integer" name="SNPs/ mismatches allowed" value="3" />
|
|
|
10 </inputs>
|
|
|
11 <outputs>
|
|
|
12 <data name="output1" format="sam" />
|
|
|
13 </outputs>
|
|
|
14 <tests>
|
|
|
15 <test>
|
|
|
16 <param name="input1" value="input.sam"/>
|
|
|
17 <output name="output1" file="output.sam"/>
|
|
|
18 </test>
|
|
|
19 </tests>
|
|
|
20 <help><![CDATA[
|
|
|
21 This program will remove mismatches from sam file.
|
|
|
22 Usage: RemoveSNPs test.sam 3
|
|
|
23 ]]></help>
|
|
|
24 <citations>
|
|
|
25 <citation type="bibtex">
|
|
|
26 @misc{RemoveSNPs,
|
|
|
27 author = {Tanwar, Deepak},
|
|
|
28 year = {2017},
|
|
|
29 title = {RemoveSNPs},
|
|
|
30 publisher = {GitHub},
|
|
|
31 journal = {GitHub repository},
|
|
|
32 url = {https://github.com/dktanwar/NGS_Sperm_H3K4me3_Planemo_tools/tree/master/01_RemoveSNPs},
|
|
|
33 }</citation>
|
|
|
34 </citations>
|
|
|
35 </tool>
|
