Mercurial > repos > iuc > transtermhp

annotate transtermhp.xml @ 1:d763e35fef0b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 4d0256dc71820b5af240f6f52ae78c9b211167f5
author iuc
date Fri, 09 Oct 2015 09:37:26 -0400
parents c28817831a24
children 1a1ec22a7e28
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c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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1 <?xml version="1.0"?>
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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2 <tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.0">
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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3 <description>finds rho-independent transcription terminators in bacterial genomes</description>
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4 <macros>
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5 <import>macros.xml</import>
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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6 </macros>
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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7 <expand macro="requirements"/>
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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8 <expand macro="stdio"/>
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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9 <command><![CDATA[
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10 #if $reference_genome.source == 'history':
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11 ln -s $reference_genome.genome_fasta genomeref.fa &&
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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12 #end if
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13
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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14 python $__tool_directory__/transtermhp.py \$TRANSTERM_EXPTERM_DAT
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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16 #if $reference_genome.source == 'cached':
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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17 "${reference_genome.fasta_indexes.fields.path}"
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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18 #elif $reference_genome.source == 'history':
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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19 genomeref.fa
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20 #end if
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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22 $input_gff3
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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24 > $output]]></command>
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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25 <inputs>
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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26 <conditional name="reference_genome">
1
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27 <param name="source" type="select" label="Reference Genome">
0
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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28 <option value="cached">Locally Cached</option>
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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29 <option value="history">From History</option>
1
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30 </param>
d763e35fef0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 4d0256dc71820b5af240f6f52ae78c9b211167f5
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31 <when value="cached">
0
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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32 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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33 <options from_data_table="all_fasta"/>
1
d763e35fef0b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 4d0256dc71820b5af240f6f52ae78c9b211167f5
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34 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
0
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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35 </param>
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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36 </when>
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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37 <when value="history">
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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38 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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39 </when>
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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40 </conditional>
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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41 <param name="input_gff3" type="data" format="gff3" label="GFF3 formatted Gene Calls"/>
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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42
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43 <!-- Currently we do not support ANY of the command line options for
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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44 TransTermHP due to the following statement:
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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45
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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46 As mentioned above, if you change any of the basic scoring
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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47 function and search parameters and are using the version 2.0
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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48 confidence scheme (recommended) then you have to recompute
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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49 the values in the expterm.dat file. If you have python
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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50 installed this is easy (though perhaps time consuming).
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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51
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52 ref: http://manpages.ubuntu.com/manpages/precise/man1/transterm.1.html
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53
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54 This is a TODO item that would be nice to get around to eventually
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55 (perhaps when a user demands it.)
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56 -->
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57 </inputs>
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58 <outputs>
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59 <data format="gff3" name="output"/>
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="source" value="history" />
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64 <param name="genome_fasta" value="sequence.fasta" />
c28817831a24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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65 <param name="input_gff3" value="sequence.gff3" />
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66 <output name="output" file="sequence.gff3.out" />
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70 **What it does**
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71
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72 Finds rho-independent transcription terminators in bacterial genomes.
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73 ]]></help>
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74 <citations>
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75 <citation type="doi">doi:10.1186/gb-2007-8-2-r22</citation>
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76 </citations>
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77 </tool>