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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4-dirty
author matthias
date Thu, 09 May 2019 16:46:52 -0400
parents fce2e761129d
children
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7bd52e7ca02c planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4-dirty
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1 <tool id="mitos" name="MITOS" version="1.0.1+galaxy1">
0
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2 <description>de-novo annotation of metazoan mitochondrial genomes</description>
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3 <!--Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc.-->
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4 <edam_topics>
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5 <edam_topic>topic_0114</edam_topic>
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6 </edam_topics>
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7 <!--Annotate a genome sequence with terms from a controlled vocabulary-->
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8 <edam_operations>
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9 <edam_operation>operation_0362</edam_operation>
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10 </edam_operations>
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11 <requirements>
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12 <requirement type="package" version="1.0.1">mitos</requirement>
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13 <requirement type="package">zip</requirement>
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14 </requirements>
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15 <version_command>python usage: %prog [options] --version</version_command>
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16 <command detect_errors="aggressive"><![CDATA[
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17 mkdir outdir &&
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18
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19 runmitos.py
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20 --input '$input'
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21 --code $code
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22 --outdir outdir
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23 --refdir /home/maze/workspace/mtdb/data/
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24 #if not "prot" in $advanced.featuretypes
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25 --noprot
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26 #end if
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27 #if not "trna" in $advanced.featuretypes
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28 --notrna
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29 #end if
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30 #if not "rrna" in $advanced.featuretypes
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31 --norrna
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32 #end if
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33 --finovl $advanced.finovl
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34 --evalue $advanced_prot.evalue
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35 --cutoff $advanced_prot.cutoff
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36 #set maxovl=float($advanced_prot.maxovl)/100.0
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37 --maxovl $maxovl
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38 --clipfac $advanced_prot.clipfac
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39 #set fragovl=float($advanced_prot.fragovl)/100.0
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40 --fragovl $fragovl
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41 --fragfac $advanced_prot.fragfac
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42 --ststrange $advanced_prot.ststrange
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43
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44 #if "zip" in $outputs:
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45 zip -9 -y -r output.zip output/"
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46 #end if
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47
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48 ]]></command>
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49 <inputs>
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50 <param argument="--input" label="Sequences" optional="false" type="data" format="fasta"/>
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51 <param argument="--code" label="Genetic code" name="code" type="select">
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52 <option value="2">Vertebrate</option>
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53 <option value="4">Mold, Protozoan, Coelenteral</option>
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54 <option value="5">Invertebrate</option>
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55 <option value="9">Echinoderm, Flatworm</option>
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56 <option value="13">Ascidian</option>
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57 <option value="14">Alternative Flatworm</option>
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58 </param>
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59 <section name="advanced" title="Advanced options">
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60 <param name="featuretypes" label="Feature types" help="Feature types that should be predicted by MITOS" type="select" multiple="true">
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61 <option value="prot" selected="true">Proteins</option>
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62 <option value="trna" selected="true">tRNAs</option>
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63 <option value="rrna" selected="true">rRNAs</option>
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64 </param>
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65 <param argument="--finovl" label="Final overlap (nt)" help="Maximum number of nucleotides by which genes of different types may overlap" type="integer" value="35" min="0"/>
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66 </section>
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67 <section name="advanced_prot" title="Advanced options for protein coding gene prediction">
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68 <param argument="--evalue" label="BLAST E-value Exponent" help="Negation of the exponent of the E-value threshold used by BLAST, i.e. a value X gives an E-value of 10^(-X)" type="float" value="2" min="0"/>
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69 <param argument="--cutoff" label="Quality cutoff" help="Minimum allowed quality in % of the maximum quality value per reading frame" type="integer" value="50" min="0" max="100"/>
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70 <param argument="--maxovl" label="Maximum overlap" help="Maximum allowed overlap of proteins in percent of the smaller feature " type="integer" value="20" min="0" max="100"/>
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71 <param argument="--clipfac" label="Clipping factor" help="Clip overlapping proteins with the same name that differ by less than the specified factor" type="float" value="10" min="0"/>
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72 <param argument="--fragovl" label="Fragment overlap" help="Maximum allowed overlap of proteins in the query (in percent of the shorter query range) for two hits to be counted as fragments of the same gene" type="integer" value="20" min="0" max="100"/>
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73 <param argument="--fragfac" label="Fragment quality factor" help="Maximum factor by which fragments of the same protein may differ in their quality" type="float" value="10"/>
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74 <param argument="--ststrange" label="Start/stop range" help="Number of aminoacids searched for start and stop codon of proteins" type="integer" value="6"/>
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75 </section>
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76 <param name="outputs" type="select" multiple="true" label="Additional outputs">
1
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77 <option value="mito">mito</option>
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78 <option value="seq">SEQ</option>
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79 <option value="raw">zipped raw results</option>
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80 </param>
0
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81 </inputs>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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82 <outputs>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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83 <data name="bedout" format="bed" from_work_dir="outdir/result.bed"/>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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84 <data name="seqout" format="txt" from_work_dir="outdir/result.seq">
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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85 <filter>"seq" in outputs</filter>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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86 </data>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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87 <data name="mitoout" format="tabular" from_work_dir="outdir/result">
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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88 <filter>"mito" in outputs</filter>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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89 </data>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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90 <data name="rawout" format="zip" from_work_dir="outdir.zip">
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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91 <filter>"raw" in outputs</filter>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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92 </data>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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93 </outputs>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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94 <help><![CDATA[
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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95 TODO: Write help
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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96 ]]></help>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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97 <citations>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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98 <citation type="doi">10.1016/j.ympev.2012.08.023</citation>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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99 </citations>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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100 </tool>
fce2e761129d planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/master/tools/mitos commit a7354d02377105590891f7337f472dc2a2f224a4
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101