Mercurial > repos > iuc > transtermhp
comparison transtermhp.xml @ 0:c28817831a24 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
| author | iuc |
|---|---|
| date | Fri, 09 Oct 2015 09:22:42 -0400 |
| parents | |
| children | d763e35fef0b |
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| -1:000000000000 | 0:c28817831a24 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.0"> | |
| 3 <description>finds rho-independent transcription terminators in bacterial genomes</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <expand macro="stdio"/> | |
| 9 <command><![CDATA[ | |
| 10 #if $reference_genome.source == 'history': | |
| 11 ln -s $reference_genome.genome_fasta genomeref.fa && | |
| 12 #end if | |
| 13 | |
| 14 python $__tool_directory__/transtermhp.py \$TRANSTERM_EXPTERM_DAT | |
| 15 | |
| 16 #if $reference_genome.source == 'cached': | |
| 17 "${reference_genome.fasta_indexes.fields.path}" | |
| 18 #elif $reference_genome.source == 'history': | |
| 19 genomeref.fa | |
| 20 #end if | |
| 21 | |
| 22 $input_gff3 | |
| 23 | |
| 24 > $output]]></command> | |
| 25 <inputs> | |
| 26 <conditional name="reference_genome"> | |
| 27 <param name="source" type="select" label="Reference Genome"> | |
| 28 <option value="cached">Locally Cached</option> | |
| 29 <option value="history">From History</option> | |
| 30 </param> | |
| 31 <when value="cached"> | |
| 32 <param name="fasta_indexes" type="select" label="Source FASTA Sequence"> | |
| 33 <options from_data_table="all_fasta"/> | |
| 34 </param> | |
| 35 </when> | |
| 36 <when value="history"> | |
| 37 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/> | |
| 38 </when> | |
| 39 </conditional> | |
| 40 <param name="input_gff3" type="data" format="gff3" label="GFF3 formatted Gene Calls"/> | |
| 41 | |
| 42 <!-- Currently we do not support ANY of the command line options for | |
| 43 TransTermHP due to the following statement: | |
| 44 | |
| 45 As mentioned above, if you change any of the basic scoring | |
| 46 function and search parameters and are using the version 2.0 | |
| 47 confidence scheme (recommended) then you have to recompute | |
| 48 the values in the expterm.dat file. If you have python | |
| 49 installed this is easy (though perhaps time consuming). | |
| 50 | |
| 51 ref: http://manpages.ubuntu.com/manpages/precise/man1/transterm.1.html | |
| 52 | |
| 53 This is a TODO item that would be nice to get around to eventually | |
| 54 (perhaps when a user demands it.) | |
| 55 --> | |
| 56 </inputs> | |
| 57 <outputs> | |
| 58 <data format="gff3" name="output"/> | |
| 59 </outputs> | |
| 60 <tests> | |
| 61 <test> | |
| 62 <param name="source" value="history" /> | |
| 63 <param name="genome_fasta" value="sequence.fasta" /> | |
| 64 <param name="input_gff3" value="sequence.gff3" /> | |
| 65 <output name="output" file="sequence.gff3.out" /> | |
| 66 </test> | |
| 67 </tests> | |
| 68 <help><![CDATA[ | |
| 69 **What it does** | |
| 70 | |
| 71 Finds rho-independent transcription terminators in bacterial genomes. | |
| 72 ]]></help> | |
| 73 <citations> | |
| 74 <citation type="doi">doi:10.1186/gb-2007-8-2-r22</citation> | |
| 75 </citations> | |
| 76 </tool> |