Mercurial > repos > iuc > transtermhp

annotate transtermhp.xml @ 6:42b38f6d9f68 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 91a178ddfde8cc9d6ca5224685a989c5618096fe
author iuc
date Tue, 12 Mar 2024 08:09:36 +0000
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1 <tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.1">
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2 <description>finds rho-independent transcription terminators in bacterial genomes</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[
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10 ## fix for TRANSTERMHP not set on containers
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11 TRANSTERMHP=\${TRANSTERMHP:-\$(dirname \$(command -v transterm))/../data/expterm.dat} &&
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12 #if $reference_genome.source == 'history':
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13 ln -s '$reference_genome.genome_fasta' genomeref.fa &&
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14 #end if
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16 python '$__tool_directory__/transtermhp.py' \$TRANSTERMHP
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18 #if $reference_genome.source == 'cached':
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19 '${reference_genome.fasta_indexes.fields.path}'
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20 #elif $reference_genome.source == 'history':
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21 genomeref.fa
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22 #end if
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23
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24 '$input_gff3'
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25 > '$output'
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26 ]]></command>
0
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27 <inputs>
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28 <conditional name="reference_genome">
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29 <param name="source" type="select" label="Reference Genome">
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30 <option value="cached">Locally Cached</option>
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31 <option value="history">From History</option>
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32 </param>
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33 <when value="cached">
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34 <param name="fasta_indexes" type="select" label="Source FASTA Sequence">
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35 <options from_data_table="all_fasta"/>
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36 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
0
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37 </param>
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38 </when>
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39 <when value="history">
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40 <param name="genome_fasta" type="data" format="fasta" label="Source FASTA Sequence"/>
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41 </when>
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42 </conditional>
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43 <param name="input_gff3" type="data" format="gff3" label="GFF3 formatted Gene Calls"/>
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44
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45 <!-- 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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46 TransTermHP due to the following statement:
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47
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48 As mentioned above, if you change any of the basic scoring
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49 function and search parameters and are using the version 2.0
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50 confidence scheme (recommended) then you have to recompute
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51 the values in the expterm.dat file. If you have python
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52 installed this is easy (though perhaps time consuming).
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53
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54 ref: http://manpages.ubuntu.com/manpages/precise/man1/transterm.1.html
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55
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56 This is a TODO item that would be nice to get around to eventually
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57 (perhaps when a user demands it.)
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58 -->
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59 </inputs>
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60 <outputs>
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61 <data format="gff3" name="output"/>
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62 </outputs>
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63 <tests>
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64 <test>
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65 <param name="source" value="history" />
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66 <param name="genome_fasta" value="sequence.fasta" />
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67 <param name="input_gff3" value="sequence.gff3" />
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68 <output name="output" file="sequence.gff3.out" />
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69 </test>
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70 </tests>
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71 <help><![CDATA[
0
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72 **What it does**
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73
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74 Finds rho-independent transcription terminators in bacterial genomes.
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75 ]]></help>
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76 <citations>
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77 <citation type="doi">doi:10.1186/gb-2007-8-2-r22</citation>
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78 </citations>
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79 </tool>