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comparison transtermhp.xml @ 3:1a1ec22a7e28 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
author iuc
date Wed, 07 Jun 2017 07:53:53 -0400
parents d763e35fef0b
children 012171ba9fce
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2:1d8ad7599f02 3:1a1ec22a7e28
1 <?xml version="1.0"?> 1 <tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.1">
2 <tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.0"> 2 <description>finds rho-independent transcription terminators in bacterial genomes</description>
3 <description>finds rho-independent transcription terminators in bacterial genomes</description> 3 <macros>
4 <macros> 4 <import>macros.xml</import>
5 <import>macros.xml</import> 5 </macros>
6 </macros> 6 <expand macro="requirements"/>
7 <expand macro="requirements"/> 7 <expand macro="stdio"/>
8 <expand macro="stdio"/> 8 <command><![CDATA[
9 <command><![CDATA[
10 #if $reference_genome.source == 'history': 9 #if $reference_genome.source == 'history':
11 ln -s $reference_genome.genome_fasta genomeref.fa && 10 ln -s '$reference_genome.genome_fasta' genomeref.fa &&
12 #end if 11 #end if
13 12
14 python $__tool_directory__/transtermhp.py \$TRANSTERM_EXPTERM_DAT 13 python '$__tool_directory__/transtermhp.py' \$TRANSTERMHP
15 14
16 #if $reference_genome.source == 'cached': 15 #if $reference_genome.source == 'cached':
17 "${reference_genome.fasta_indexes.fields.path}" 16 '${reference_genome.fasta_indexes.fields.path}'
18 #elif $reference_genome.source == 'history': 17 #elif $reference_genome.source == 'history':
19 genomeref.fa 18 genomeref.fa
20 #end if 19 #end if
21 20
22 $input_gff3 21 '$input_gff3'
23 22 > '$output'
24 > $output]]></command> 23 ]]></command>
25 <inputs> 24 <inputs>
26 <conditional name="reference_genome"> 25 <conditional name="reference_genome">
27 <param name="source" type="select" label="Reference Genome"> 26 <param name="source" type="select" label="Reference Genome">
28 <option value="cached">Locally Cached</option> 27 <option value="cached">Locally Cached</option>
29 <option value="history">From History</option> 28 <option value="history">From History</option>
52 ref: http://manpages.ubuntu.com/manpages/precise/man1/transterm.1.html 51 ref: http://manpages.ubuntu.com/manpages/precise/man1/transterm.1.html
53 52
54 This is a TODO item that would be nice to get around to eventually 53 This is a TODO item that would be nice to get around to eventually
55 (perhaps when a user demands it.) 54 (perhaps when a user demands it.)
56 --> 55 -->
57 </inputs> 56 </inputs>
58 <outputs> 57 <outputs>
59 <data format="gff3" name="output"/> 58 <data format="gff3" name="output"/>
60 </outputs> 59 </outputs>
61 <tests> 60 <tests>
62 <test> 61 <test>
63 <param name="source" value="history" /> 62 <param name="source" value="history" />
64 <param name="genome_fasta" value="sequence.fasta" /> 63 <param name="genome_fasta" value="sequence.fasta" />
65 <param name="input_gff3" value="sequence.gff3" /> 64 <param name="input_gff3" value="sequence.gff3" />
66 <output name="output" file="sequence.gff3.out" /> 65 <output name="output" file="sequence.gff3.out" />
67 </test> 66 </test>
68 </tests> 67 </tests>
69 <help><![CDATA[ 68 <help><![CDATA[
70 **What it does** 69 **What it does**
71 70
72 Finds rho-independent transcription terminators in bacterial genomes. 71 Finds rho-independent transcription terminators in bacterial genomes.
73 ]]></help> 72 ]]></help>
74 <citations> 73 <citations>