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comparison compalignp.xml @ 0:7e55ac3bd458 draft

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author rnateam
date Tue, 09 Jun 2015 05:36:03 -0400
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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>