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/tools/regVariation/substitutions.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 38 lines | 29 code | 9 blank | 0 comment | 0 complexity | 5debced86330e9c928442edb473ae435 MD5 | raw file
 1<tool id="substitutions1" name="Fetch substitutions " version="1.0.0">
 2  <description> from pairwise alignments</description>
 3  <command interpreter="python">
 4  	substitutions.py 
 5  	$input 
 6  	$out_file1
 7  </command>
 8  <inputs>
 9    <param format="maf" name="input" type="data" label="Select pair-wise alignment data"/>
10  </inputs>
11  <outputs>
12    <data format="tabular" name="out_file1" metadata_source="input"/>
13  </outputs>
14
15  <tests>
16    <test>
17      <param name="input" value="Interval2Maf_pairwise_out.maf"/>
18      <output name="out_file1" file="subs.out"/>
19    </test>
20  </tests>
21 <help> 
22
23.. class:: infomark
24
25**What it does**
26
27This tool takes a pairwise MAF file as input and fetches substitutions per alignment block.
28
29-----
30
31.. class:: warningmark
32
33**Note**
34
35Any block/s not containing exactly two sequences, will be omitted. 
36
37  </help>  
38</tool>