Mercurial > repos > iuc > jcvi_gff_stats

annotate jcvi_gff_stats.xml @ 0:2defe48e4c7a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
author iuc
date Thu, 02 Aug 2018 09:57:30 -0400
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children 8cffbd184762
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2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
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1 <?xml version="1.0"?>
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2 <tool id="jcvi_gff_stats" name="Genome annotation statistics" profile="16.04" version="@VERSION@">
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3 <description></description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command><![CDATA[
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9
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10 ln -s '${gff}' 'input.gff'
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11
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12 &&
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14 python -m jcvi.annotation.stats genestats 'input.gff' > '${summary}'
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16 &&
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17
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18 #if str($ref_genome.genome_type_select) == "indexed":
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19 python -m jcvi.annotation.stats summary 'input.gff' '${ref_genome.genome.fields.path}' 2>&1 | tail -n +3 >> '${summary}'
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
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20 #else
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21 python -m jcvi.annotation.stats summary 'input.gff' '${ref_genome.genome}' 2>&1 | tail -n +3 >> '${summary}'
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22 #end if
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23
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24 &&
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25
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26 python -m jcvi.annotation.stats stats 'input.gff' 2>&1 | grep Mean >> '${summary}'
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28 &&
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29
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30 python -m jcvi.annotation.stats histogram 'input.gff'
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32 &&
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33
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34 pdfunite *.input.pdf '${graphs}'
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35 ]]></command>
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36 <inputs>
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37 <param name="gff" type="data" format="gff" label="Annotation to analyse"/>
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38 <conditional name="ref_genome">
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39 <param label="Reference genome" name="genome_type_select" type="select">
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40 <option selected="True" value="indexed">Use a built-in genome</option>
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41 <option value="history">Use a genome from history</option>
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42 </param>
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43 <when value="indexed">
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44 <param
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45 help="If your genome of interest is not listed, contact the Galaxy server administrators"
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46 label="Select a reference genome"
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47 name="genome"
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48 type="select"
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49 >
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50 <options from_data_table="all_fasta">
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51 <filter column="2" type="sort_by" />
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52 <validator message="No genomes are available" type="no_options" />
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53 </options>
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54 </param>
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55 </when>
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56 <when value="history">
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57 <param name="genome" type="data" format="fasta" label="Corresponding genome sequence"/>
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58 </when>
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59 </conditional>
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60 </inputs>
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61 <outputs>
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62 <data format="txt" name="summary" label="${tool.name} on ${on_string}: summary"/>
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63 <data format="pdf" name="graphs" label="${tool.name} on ${on_string}: gene length"/>
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="gff" value="annot.gff3"/>
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68 <conditional name="ref_genome">
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69 <param name="genome_type_select" value="history"/>
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70 <param name="genome" value="genome.fasta"/>
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71 </conditional>
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72 <output name="summary" file="summary.txt"/>
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73 <output name="graphs" file="all.pdf" compare="sim_size"/>
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74 </test>
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75 <test>
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76 <param name="gff" value="annot.gff3"/>
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77 <conditional name="ref_genome">
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78 <param name="genome_type_select" value="indexed"/>
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79 <param name="genome" value="merlin"/>
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80 </conditional>
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81 <output name="summary" file="summary.txt"/>
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82 <output name="graphs" file="all.pdf" compare="sim_size"/>
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83 </test>
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84 </tests>
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85 <help><![CDATA[
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
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86 Based on JCVI Python utility libraries on genome assembly, annotation and comparative genomics.
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
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87
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
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88 .. _JCVI Python utilities: https://github.com/tanghaibao/jcvi
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
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89 ]]></help>
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
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90 <expand macro="citations"/>
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
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91 </tool>