Mercurial > repos > bgruening > glimmer_not_knowledge_based
annotate glimmer_wo_icm.xml @ 2:73c58e2debd0 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 274d1f6804bfd0362fdcd2383bfdb32ca8fd634e"
author | iuc |
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date | Sun, 20 Mar 2022 10:08:30 +0000 |
parents | 4da5f6bdcf12 |
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4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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1 <tool id="glimmer_not_knowledge_based" name="Glimmer3" version="@WRAPPER_VERSION@"> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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2 <description>Predict ORFs in prokaryotic genomes (not knowlegde-based)</description> |
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73c58e2debd0
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 274d1f6804bfd0362fdcd2383bfdb32ca8fd634e"
iuc
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3 <expand macro="bio_tools"/> |
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4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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4 <macros> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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5 <import>macros.xml</import> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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6 </macros> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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7 <expand macro="requirements"/> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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8 <command><![CDATA[ |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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9 python '$__tool_directory__/glimmer_wo_icm.py' |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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10 '$input' |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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11 #if $report: |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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12 '$prediction' |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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13 #else: |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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14 'None' |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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15 #end if |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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16 #if $detailed_report: |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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17 '$detailed' |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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18 #else: |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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19 'None' |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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20 #end if |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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21 $overlap |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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22 $gene_length |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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23 $threshold |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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24 $linear |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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25 '$genes_output' |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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26 ]]></command> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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27 <inputs> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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28 <param name="input" type="data" format="fasta" label="Genome sequence" /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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29 <param name="overlap" type="integer" value="0" label="Set maximum overlap length. Overlaps this short or shorter are ignored." /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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30 <param name="gene_length" type="integer" value="110" label="Set minimum gene length." /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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31 <param name="threshold" type="integer" value="30" label="Set threshold score for calling as gene. If the in-frame score >= N, then the region is given a number and considered a potential gene." /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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32 <param name="linear" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Assume linear rather than circular genome, i.e., no wraparound" /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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33 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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34 <param name="detailed_report" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a detailed gene prediction report as separate file" /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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35 <param name="report" type="boolean" truevalue="" falsevalue="" checked="false" label="Report the classic glimmer table output" /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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36 </inputs> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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37 <outputs> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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38 <data name="genes_output" format="fasta" label="Glimmer3 on ${on_string} (Gene Prediction FASTA)" /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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39 <data name="prediction" format="txt" label="Glimmer3 on ${on_string} (Gene Prediction table)"> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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40 <filter>report == True</filter> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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41 </data> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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42 <data name="detailed" format="txt" label="Glimmer3 on ${on_string} (detailed report)"> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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43 <filter>detailed_report == True</filter> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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44 </data> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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45 </outputs> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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46 <tests> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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47 <test> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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48 <param name="input" value="streptomyces_Tue6071_plasmid_genomic.fasta" /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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49 <param name="overlap" value="0" /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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50 <param name="gene_length" value="110" /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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51 <param name="threshold" value="30" /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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52 <param name="linear" value="true" /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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53 <param name="detailed_report" value="" /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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54 <param name="report" value="" /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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55 <output name="genes_output" file="glimmer_wo_icm_trans-table-11_plasmid_genomic.fasta" ftype="fasta" /> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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56 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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57 </tests> |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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58 <help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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59 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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60 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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61 **What it does** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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62 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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63 This tool predicts open reading frames (ORFs) from a given DNA Sequence. That tool is not knowlegde-based. |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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64 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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65 The recommended way is to use a trained Glimmer3 with ICM model. Use the knowlegde-based version for that and insert/generate a training set. |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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66 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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67 ----- |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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68 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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69 **Glimmer Overview** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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70 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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71 :: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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72 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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73 ************** ************** ************** ************** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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74 * * * * * * * * |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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75 * long-orfs * ===> * Extract * ===> * build-icm * ===> * glimmer3 * |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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76 * * * * * * * * |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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77 ************** ************** ************** ************** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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78 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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79 ----- |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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80 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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81 **Example** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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82 |
4da5f6bdcf12
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/glimmer commit 37388949e348d221170659bbee547bf4ac67ef1a
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83 Suppose you have the following DNA sequences:: |
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84 |
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85 >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other; |
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86 cccgcggagcgggtaccacatcgctgcgcgatgtgcgagcgaacacccgggctgcgcccg |
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87 ggtgttgcgctcccgctccgcgggagcgctggcgggacgctgcgcgtcccgctcaccaag |
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88 cccgcttcgcgggcttggtgacgctccgtccgctgcgcttccggagttgcggggcttcgc |
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89 cccgctaaccctgggcctcgcttcgctccgccttgggcctgcggcgggtccgctgcgctc |
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90 ccccgcctcaagggcccttccggctgcgcctccaggacccaaccgcttgcgcgggcctgg |
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91 ....... |
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92 |
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93 Running this tool will produce a FASTA file with predicted genes and glimmer output files like the following:: |
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94 |
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95 >SQ Sequence 8667507 BP; 1203558 A; 3121252 C; 3129638 G; 1213059 T; 0 other; |
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96 orf00001 577 699 +1 5.24 |
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97 orf00003 800 1123 +2 5.18 |
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98 orf00004 1144 3813 +1 10.62 |
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99 orf00006 3857 6220 +2 6.07 |
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100 orf00007 6226 7173 +1 1.69 |
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101 orf00008 7187 9307 +2 8.95 |
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102 orf00009 9424 10410 +1 8.29 |
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103 orf00010 10515 11363 +3 7.00 |
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104 orf00011 11812 11964 +1 2.80 |
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105 orf00012 12360 13457 +3 4.80 |
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106 orf00013 14379 14044 -1 7.41 |
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107 orf00015 15029 14739 -3 12.43 |
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108 orf00016 15066 15227 +3 1.91 |
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109 orf00020 16061 15351 -3 2.83 |
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110 orf00021 17513 17391 -3 2.20 |
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111 orf00023 17529 17675 +3 0.11 |
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112 |
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113 |
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114 |
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115 ]]> |
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116 </help> |
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117 <expand macro="citation" /> |
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118 </tool> |