Mercurial > repos > bgruening > glimmer_build_icm
annotate glimmer_build_icm.xml @ 0:9c195b26a5ac draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
author | bgruening |
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date | Tue, 28 Nov 2017 10:08:06 -0500 |
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children | cc51783dc93c |
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9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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1 <tool id="glimmer_build_icm" name="Glimmer ICM builder" version="@WRAPPER_VERSION@"> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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2 <description></description> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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3 <macros> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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4 <import>macros.xml</import> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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5 </macros> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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6 <expand macro="requirements"/> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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7 <command><![CDATA[ |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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8 build-icm |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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9 --depth $depth |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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10 $no_stops |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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11 --period $period |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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12 --width $width |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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13 |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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14 #if $stop_codon_opts.stop_codon_opts_selector == "gb": |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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15 --trans_table '${stop_codon_opts.genbank_gencode}' |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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16 #else: |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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17 --stop_codons '${stop_codon_opts.stop_codons}' |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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18 #end if |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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19 |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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20 '$outfile' < '$infile' 2>&1; |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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21 ]]></command> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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22 <inputs> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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23 <param name="infile" type="data" format="fasta" label="Trainings Dataset" help="A set of known genes in FASTA format." /> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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24 <param name="depth" type="integer" value="7" label="Set the depth of the ICM" help="The depth is the maximum number of positions in the context window that will be used to determine the probability of the predicted position." /> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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25 <param name="period" type="integer" value="3" label="Set the period of the ICM" help="The period is the number of different submodels for different positions in the text in a cyclic pattern. E.g., if the period is 3, the first submodel will determine positions 1, 4, 7, ..." /> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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26 <param name="width" type="integer" value="12" label="Set the width of the ICM" help="The width includes the predicted position." /> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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27 <param name="no_stops" type="boolean" truevalue="--no_stops" falsevalue="" checked="false" label="Do not use any input strings with in-frame stop codons" /> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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28 |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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29 <conditional name="stop_codon_opts"> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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30 <param name="stop_codon_opts_selector" type="select" label="Specify start codons as"> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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31 <option value="gb" selected="True">Genbank translation table entry</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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32 <option value="free_form">Comma-separated list</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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33 </param> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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34 <when value="gb"> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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35 <param name="genbank_gencode" type="select" label="Use Genbank translation table to specify stop codons"> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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36 <option value="1" selected="True">1. Standard</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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37 <option value="2">2. Vertebrate Mitochondrial</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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38 <option value="3">3. Yeast Mitochondrial</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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39 <option value="4">4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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40 <option value="5">5. Invertebrate Mitochondrial</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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41 <option value="6">6. Ciliate, Dasycladacean and Hexamita Nuclear Code</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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42 <option value="9">9. Echinoderm Mitochondrial</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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43 <option value="10">10. Euplotid Nuclear</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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44 <option value="11">11. Bacteria and Archaea</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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45 <option value="12">12. Alternative Yeast Nuclear</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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46 <option value="13">13. Ascidian Mitochondrial</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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47 <option value="14">14. Flatworm Mitochondrial</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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48 <option value="15">15. Blepharisma Macronuclear</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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49 <option value="16">16. Chlorophycean Mitochondrial</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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50 <option value="21">21. Trematode Mitochondrial</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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51 <option value="22">22. Scenedesmus obliquus mitochondrial</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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52 <option value="23">23. Thraustochytrium Mitochondrial</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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53 <option value="24">24. Pterobranchia mitochondrial</option> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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54 </param> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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55 </when> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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56 <when value="free_form"> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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57 <param name="stop_codons" type="text" value="tag,tga,taa" label="Specify stop codons as a comma-separated list" /> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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58 </when> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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59 </conditional> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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60 </inputs> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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61 <outputs> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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62 <data format="data" name="outfile" /> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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63 </outputs> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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64 <tests> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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65 <test> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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66 <param name="infile" value='streptomyces_Tu6071_plasmid_genes.fasta' /> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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67 <param name="depth" value="7" /> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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68 <param name="period" value="3" /> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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69 <param name="width" value="12" /> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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70 <param name="no_stops" value="" /> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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71 <param name="genbank_gencode" value="11" /> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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72 <!-- compare files sizes, because the output is a binary --> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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73 <output name="outfile" file='streptomyces_Tu6071_plasmid_genes.icm' compare="sim_size" delta="1000" ftype="data" /> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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74 </test> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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75 </tests> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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76 |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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77 <help> |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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78 <![CDATA[ |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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79 |
9c195b26a5ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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80 **What it does** |
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81 |
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82 This program constructs an interpolated context model (ICM) from an input set of sequences. |
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83 |
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84 This model can be used by Glimmer3 to predict genes. |
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85 |
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86 **TIP** To extract CDS from a GenBank file use the tool *Extract ORF from a GenBank file*. |
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87 |
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88 ----- |
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89 |
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90 **Example** |
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91 |
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92 *Input*:: |
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93 |
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94 - Genome Sequence |
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95 |
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96 >CELF22B7 C.aenorhabditis elegans (Bristol N2) cosmid F22B7 |
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97 GATCCTTGTAGATTTTGAATTTGAAGTTTTTTCTCATTCCAAAACTCTGT |
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98 GATCTGAAATAAAATGTCTCAAAAAAATAGAAGAAAACATTGCTTTATAT |
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99 TTATCAGTTATGGTTTTCAAAATTTTCTGACATACCGTTTTGCTTCTTTT |
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100 TTTCTCATCTTCTTCAAATATCAATTGTGATAATCTGACTCCTAACAATC |
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101 GAATTTCTTTTCCTTTTTCTTTTTCCAACAACTCCAGTGAGAACTTTTGA |
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102 ATATCTTCAAGTGACTTCACCACATCAGAAGGTGTCAACGATCTTGTGAG |
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103 AACATCGAATGAAGATAATTTTAATTTTAGAGTTACAGTTTTTCCTCCGA |
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104 CAATTCCTGATTTACGAACATCTTCTTCAAGCATTCTACAGATTTCTTGA |
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105 TGCTCTTCTAGGAGGATGTTGAAATCCGAAGTTGGAGAAAAAGTTCTCTC |
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106 AACTGAAATGCTTTTTCTTCGTGGATCCGATTCAGATGGACGACCTGGCA |
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107 GTCCGAGAGCCGTTCGAAGGAAAGATTCTTGTGAGAGAGGCGTGAAACAC |
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108 AAAGGGTATAGGTTCTTCTTCAGATTCATATCACCAACAGTTTGAATATC |
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109 CATTGCTTTCAGTTGAGCTTCGCATACACGACCAATTCCTCCAACCTAAA |
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110 AAATTATCTAGGTAAAACTAGAAGGTTATGCTTTAATAGTCTCACCTTAC |
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111 GAATCGGTAAATCCTTCAAAAACTCCATAATCGCGTTTTTATCATTTTCT |
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112 ..... |
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113 |
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114 *Output*:: |
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115 interpolated context model (ICM) |
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116 |
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117 |
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118 |
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119 ]]> |
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120 </help> |
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121 <expand macro="citation" /> |
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122 </tool> |