|
0
|
1 <tool id="compalignp" name="Compalignp" version="1.0">
|
|
|
2 <description>Fractional identities between alignments</description>
|
|
|
3 <requirements>
|
|
|
4 <requirement type="package" version="1.0">compalignp</requirement>
|
|
|
5 </requirements>
|
|
|
6 <stdio>
|
|
|
7 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
|
|
|
8 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
|
|
|
9 </stdio>
|
|
|
10 <command>
|
|
|
11 <![CDATA[
|
|
|
12 compalignp
|
|
|
13 -t $rna_alignment_target
|
|
|
14 -r $rna_alignment_reference
|
|
|
15 > $output
|
|
|
16 ]]>
|
|
|
17 </command>
|
|
|
18 <inputs>
|
|
|
19 <param format="clustalw,stockholm" name="rna_alignment_target" type="data" label="Target RNA Alignment" help="(-t)" />
|
|
|
20 <param format="clustalw,stockholm" name="rna_alignment_reference" type="data" label="Reference RNA Alignment" help="(-r)" />
|
|
|
21 </inputs>
|
|
|
22 <outputs>
|
|
|
23 <data name="output" format="txt" />
|
|
|
24 </outputs>
|
|
|
25 <tests>
|
|
|
26 <test>
|
|
|
27 <param name="rna_alignment_target" value="eukaryotic-trnas_2.1.clustal"/>
|
|
|
28 <param name="rna_alignment_reference" value="eukaryotic-trnas_2.1.clustal"/>
|
|
|
29 <output name="output" file="eukaryotic-trnas_2.1.out"/>
|
|
|
30 </test>
|
|
|
31 </tests>
|
|
|
32 <help>
|
|
|
33 <![CDATA[
|
|
|
34 **compalignp**
|
|
|
35
|
|
|
36 > Paranoia version of squids compalign.
|
|
|
37
|
|
|
38 Compute fractional "identity" between trusted alignment and test alignment
|
|
|
39 Identity of the multiple sequence alignments is defined as
|
|
|
40 the averaged identity over all N(N-1)/2 pairwise alignments.
|
|
|
41
|
|
|
42
|
|
|
43 ]]>
|
|
|
44 </help>
|
|
|
45 <citations>
|
|
|
46 <citation type="doi">10.1186/1748-7188-1-19</citation>
|
|
|
47 </citations>
|
|
|
48 </tool>
|
