Mercurial > repos > iuc > transtermhp
annotate transtermhp.xml @ 4:9a90656a1af9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
author | iuc |
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date | Tue, 30 Oct 2018 20:25:05 -0400 |
parents | 1a1ec22a7e28 |
children | 012171ba9fce |
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1a1ec22a7e28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
iuc
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1 <tool id="transtermhp" name="TransTermHP" version="@WRAPPER_VERSION@.1"> |
1a1ec22a7e28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
iuc
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2 <description>finds rho-independent transcription terminators in bacterial genomes</description> |
1a1ec22a7e28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
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3 <macros> |
1a1ec22a7e28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
iuc
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4 <import>macros.xml</import> |
1a1ec22a7e28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
iuc
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5 </macros> |
1a1ec22a7e28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
iuc
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6 <expand macro="requirements"/> |
1a1ec22a7e28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
iuc
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7 <expand macro="stdio"/> |
1a1ec22a7e28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
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8 <command><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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9 #if $reference_genome.source == 'history': |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
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10 ln -s '$reference_genome.genome_fasta' genomeref.fa && |
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c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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11 #end if |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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12 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
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13 python '$__tool_directory__/transtermhp.py' \$TRANSTERMHP |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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14 |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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15 #if $reference_genome.source == 'cached': |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
iuc
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16 '${reference_genome.fasta_indexes.fields.path}' |
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c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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17 #elif $reference_genome.source == 'history': |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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18 genomeref.fa |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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19 #end if |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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20 |
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1a1ec22a7e28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
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21 '$input_gff3' |
1a1ec22a7e28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
iuc
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22 > '$output' |
1a1ec22a7e28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
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23 ]]></command> |
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c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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24 <inputs> |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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25 <conditional name="reference_genome"> |
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d763e35fef0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 4d0256dc71820b5af240f6f52ae78c9b211167f5
iuc
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26 <param name="source" type="select" label="Reference Genome"> |
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c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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27 <option value="cached">Locally Cached</option> |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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28 <option value="history">From History</option> |
1
d763e35fef0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 4d0256dc71820b5af240f6f52ae78c9b211167f5
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29 </param> |
d763e35fef0b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 4d0256dc71820b5af240f6f52ae78c9b211167f5
iuc
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30 <when value="cached"> |
0
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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31 <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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32 <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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33 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> |
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c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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34 </param> |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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35 </when> |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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36 <when value="history"> |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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37 <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
iuc
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38 </when> |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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39 </conditional> |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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40 <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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41 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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42 <!-- 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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43 TransTermHP due to the following statement: |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
iuc
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44 |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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45 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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46 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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47 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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48 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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49 installed this is easy (though perhaps time consuming). |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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50 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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51 ref: http://manpages.ubuntu.com/manpages/precise/man1/transterm.1.html |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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52 |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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53 This is a TODO item that would be nice to get around to eventually |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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54 (perhaps when a user demands it.) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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55 --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
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56 </inputs> |
1a1ec22a7e28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
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57 <outputs> |
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58 <data format="gff3" name="output"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
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59 </outputs> |
1a1ec22a7e28
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60 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
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61 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
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62 <param name="source" value="history" /> |
1a1ec22a7e28
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
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63 <param name="genome_fasta" value="sequence.fasta" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
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64 <param name="input_gff3" value="sequence.gff3" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 581d451609b919893ba53d104a5bcf2e9e565d1d
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65 <output name="output" file="sequence.gff3.out" /> |
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66 </test> |
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67 </tests> |
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68 <help><![CDATA[ |
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69 **What it does** |
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70 |
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71 Finds rho-independent transcription terminators in bacterial genomes. |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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72 ]]></help> |
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73 <citations> |
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74 <citation type="doi">doi:10.1186/gb-2007-8-2-r22</citation> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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75 </citations> |
c28817831a24
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/transtermhp commit 799339e22181d28cb2b145454d353d6025779636
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76 </tool> |