Mercurial > repos > rnateam > compalignp
comparison compalignp.xml @ 0:28a85319a3c6 draft
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| author | rnateam |
|---|---|
| date | Fri, 05 Jun 2015 05:47:06 -0400 |
| parents | |
| children | a83b11545348 |
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| -1:000000000000 | 0:28a85319a3c6 |
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| 1 <tool id="compalignp" name="Compalignp" version="1.0"> | |
| 2 <description></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 $flag_verbose | |
| 16 > $output | |
| 17 ]]> | |
| 18 </command> | |
| 19 <inputs> | |
| 20 <param format="clustalw,stockholm" name="rna_aligment_target" type="data" label="Target RNA Alignment" help="(-t)" /> | |
| 21 <param format="clustalw,stockholm" name="rna_aligment_reference" type="data" label="Reference RNA Alignment" help="(-r)" /> | |
| 22 <param name="flag_verbose" type="boolean" true-value="-v" false-value="" label="Verbose output" help="(-v)" /> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <data name="output" format="txt" /> | |
| 26 </outputs> | |
| 27 <tests> | |
| 28 <test> | |
| 29 <param name="rna_alignment_target" value="eukaryotic-trnas_2.1.clustal"/> | |
| 30 <param name="rna_alignment_reference" value="eukaryotic-trnas_2.1.clustal"/> | |
| 31 <output name="output" file="eukaryotic-trnas_2.1.out"/> | |
| 32 </test> | |
| 33 </tests> | |
| 34 <help> | |
| 35 <![CDATA[ | |
| 36 **compalignp** | |
| 37 | |
| 38 > Paranoia version of squids compalign. | |
| 39 | |
| 40 Compute fractional "identity" between trusted alignment and test alignment | |
| 41 Identity of the multiple sequence alignments is defined as | |
| 42 the averaged identity over all N(N-1)/2 pairwise alignments. | |
| 43 | |
| 44 | |
| 45 ]]> | |
| 46 </help> | |
| 47 <citations> | |
| 48 <citation type="doi">10.1186/1748-7188-1-19</citation> | |
| 49 </citations> | |
| 50 </tool> |