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annotate panaroo.xml @ 1:b6a78d286482 draft

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planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
author iuc
date Fri, 11 Apr 2025 11:23:50 +0000
parents 50483f852947
children b05be6316263
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50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
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1 <tool id="panaroo" name="Panaroo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
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2 <description>A Bacterial Pangenome Analysis Pipeline</description>
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
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3 <macros>
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4 <import>macros.xml</import>
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
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5 </macros>
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
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6 <expand macro="edam_ontology"/>
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
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7 <expand macro="biotools"/>
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
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8 <expand macro="requirements"/>
1
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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9 <command detect_errors="exit_code"><![CDATA[
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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10 mkdir outdir &&
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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11 #import re
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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12 #set input_directory = 'input_directory'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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13 mkdir $input_directory &&
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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14 #for $gff in $gff_input_collection:
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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15 #set identifier = re.sub('[^\s\w\-\\.]','_',str($gff.element_identifier))
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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16 ln -fs '$gff' '$input_directory/$identifier' &&
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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17 #end for
0
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18
1
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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19 panaroo
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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20 --clean-mode '$mode'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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21 #if str($gen_code) != 'None':
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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22 --codon-table '$gen_code'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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23 #end if
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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24 #if str($advanced.adv_options_selector) == "set":
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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25 #if $advanced.remove_invalid_genes
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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26 $advanced.remove_invalid_genes
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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27 #end if
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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28 --threshold '$advanced.matching_option.threshold'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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29 --family_threshold '$advanced.matching_option.family_threshold'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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30 --len_dif_percent '$advanced.matching_option.len_dif_percent'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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31 $advanced.matching_option.merge_paralogs
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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32 --search_radius '$advanced.refind_option.search_radius'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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33 --refind_prop_match '$advanced.refind_option.refind_prop_match'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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34 --refind-mode '$advanced.refind_option.refind_mode'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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35 --min_trailing_support '$advanced.graph_correction_option.min_trailing_support'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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36 --trailing_recursive '$advanced.graph_correction_option.trailing_recursive'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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37 --edge_support_threshold '$advanced.graph_correction_option.edge_support_threshold'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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38 --remove_by_consensus '$advanced.graph_correction_option.remove_by_consensus'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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39 --high_var_flag '$advanced.graph_correction_option.high_var_flag'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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40 --min_edge_support_sv '$advanced.graph_correction_option.min_edge_support_sv'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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41 $advanced.graph_correction_option.all_seq_in_graph
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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42 $advanced.graph_correction_option.no_clean_edges
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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43 #if $advanced.gene_alignment_option.alignment != 'None'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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44 --alignment '$advanced.gene_alignment_option.alignment'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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45 --aligner '$advanced.gene_alignment_option.aligner'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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46 #end if
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47 #if $advanced.gene_alignment_option.core_subset
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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48 --core_subset $advanced.gene_alignment_option.core_subset
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49 #end if
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50 #if $advanced.gene_alignment_option.core_entropy_filter
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51 --core_entropy_filter $advanced.gene_alignment_option.core_entropy_filter
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52 #end if
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53 #end if
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54 -i $input_directory/*.gff
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55 -o outdir
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56 -t \${GALAXY_SLOTS:-8}
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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57 #if $log_out
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58 2>&1 | tee '$log'
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59 #end if
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60 && mv outdir/gene_presence_absence.Rtab outdir/gene_presence_absence_rtab.Rtab &&
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61 mv outdir/combined_protein_cdhit_out.txt outdir/combined_protein_cdhit_out.fa
0
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62 ]]></command>
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63 <inputs>
1
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64 <param name="gff_input_collection" type="data_collection" format="gff" collection_type="list" label="GFF Input Collection" help="A collection of input GFF files"/>
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65 <param name="mode" type="select" label="The stringency mode for Panaroo to run" help="Each of these modes can be fine tuned using the additional parameters in the 'Graph correction' section.">
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66 <option value="strict">Strict</option>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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67 <option value="moderate">Moderate</option>
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68 <option value="sensitive">Sensitive</option>
0
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69 </param>
1
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70 <param name="gen_code" type="select" label="The Codon table used for translation" help="Default: 11.Bacteria and Archaea">
0
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71 <expand macro="genetic_code"/>
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72 </param>
1
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73 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
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74 <conditional name="advanced">
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75 <param name="adv_options_selector" type="select" label="Set Advanced Options?" help="Fine Tuning of Panaroo algorithmic parameters">
0
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76 <option value="set">Set</option>
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77 <option value="do_not_set" selected="True">Do not set</option>
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78 </param>
1
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79 <when value="set">
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80 <param argument="--remove-invalid-genes" type="boolean" truevalue="--remove-invalid-genes" falsevalue="" label="Remove Invalid Genes" help="Removes annotations that do not conform to the expected Prokka format."/>
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81
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82 <!--Options for Matching-->
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83 <section name="matching_option" title="Matching" expanded="false">
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84 <param argument="--threshold" type="float" value="0.98" label="Sequence identity threshold" help="default: 0.98"/>
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85 <param argument="--family_threshold" type="float" value="0.7" label="Protein family sequence identity threshold" help="default: 0.7"/>
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86 <param argument="--len_dif_percent" type="float" value="0.98" label="Length difference cutoff" help="default: 0.98"/>
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87 <param argument="--merge-paralogs" type="boolean" truevalue="--merge_paralogs" falsevalue="" label="Merge Paralogs"/>
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88 </section>
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89
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90 <!--Options for Refind-->
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91 <section name="refind_option" title="Refind" expanded="false">
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92 <param argument="--search_radius" type="integer" value="5000" label="Refinding Search radius" help="The distance in nucleotides surronding the neighbour of an accessory gene in which to search for it"/>
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93 <param argument="--refind_prop_match" type="float" value="0.2" label="Refinding Proportion Match" help="he proportion of an accessory gene that must be found in order to consider it a match"/>
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94 <param argument="--refind_mode" type="select" label="Refind Mode" help="Set the stringency mode at which to re-find genes">
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95 <option value="default" selected="True">Default</option>
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96 <option value="strict">Strict</option>
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97 <option value="off">Off</option>
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98 </param>
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99 </section>
0
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100
1
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101 <!--Graph Correction-->
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102 <section name="graph_correction_option" title="Graph Correction" expanded="false">
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103 <param argument="--min_trailing_support" type="integer" value="2" label="Minimum trailing support" help="Minimum cluster size to keep a gene called at the end of a contig"/>
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104 <param argument="--trailing_recursive" type="integer" value="1" label="Trailing Recursive" help="Number of times to perform recursive trimming of low support nodes near the end of contigs"/>
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105 <param argument="--edge_support_threshold" type="float" value="1" label="Edge support threshold" help="Minimum support required to keep an edge that has been flagged as a possible mis-assembly."/>
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106 <param argument="--len_outlier_proportion" type="float" value="0.01" label="Length outlier support proportion" help="--length_outlier_support_proportion"/>
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107 <param argument="--remove_by_consensus" type="boolean" truevalue="True" falsevalue="False" label="Remove consensus" help="If a gene is called in the same region with similar sequence a minority of the time, remove it."/>
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108 <param argument="--high_var_flag" type="integer" value="5" label="Highly variable gene region" help="Minimum number of nested cycles to call a highly variable gene region."/>
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109 <param argument="--min_edge_support_sv" type="integer" value="2" label="Minimum edge support structural variants" help="Minimum edge support required to call structural variants in the presence/absence sv file"/>
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110 <param argument="--all_seq_in_graph" type="boolean" truevalue="--all_seq_in_graph" falsevalue="" label="Retains all DNA sequence" help="Retains all DNA sequence for each gene cluster in the graph output."/>
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111 <param argument="--no_clean_edges" type="boolean" truevalue="--no_clean_edges" falsevalue="" label="No Clean Edges" help="Turn off edge filtering in the final output graph."/>
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112 </section>
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113
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114 <!--Gene Alignment-->
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115 <section name="gene_alignment_option" title="Gene Alignment" expanded="false">
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116 <param argument="--alignment" type="select" label="Output alignments of core genes or all genes.">
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117 <option value="None" selected="True">None</option>
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118 <option value="core">Core genome alignment</option>
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119 <option value="pan">Pan-genome alignment</option>
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120 </param>
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121 <param argument="--aligner" type="select" label="Specify an aligner" help="--aligner [mafft|prank|clustal][default: mafft]">
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122 <option value="mafft" selected="True">MAFFT</option>
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123 <option value="prank">PRANK</option>
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124 <option value="clustal">Clustal</option>
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125 </param>
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126 <param argument="--codons" type="boolean" label="Generate codon alignments by aligning sequences at the protein level" truevalue="--codons" falsevalue="" help="Generate codon alignments by aligning sequences at the protein level"/>
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127 <param argument="--core_threshold" type="float" value="0.95" label="Core Threshold" help="Core-genome sample threshold"/>
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128 <param argument="--core_subset" type="integer" optional="true" label="Subset of the core genome to these many genes" help="Randomly subset the core genome to these many genes. Default is all genes."/>
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129 <param argument="--core_entropy_filter" type="float" value="0.1" label="Core Entropy Filter" help="Manually set the Block Mapping and Gathering with Entropy (BMGE) filter. By default this is set using the Tukey outlier method."/>
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130 </section>
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131 </when>
0
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132 <when value="do_not_set"/>
1
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133 </conditional>
0
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134 </inputs>
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135 <outputs>
1
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136 <!--Panaroo default outputs -->
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137 <collection name="output" type="list" label="${tool.name} on ${on_string}: Pangenome default output">
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138 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta$" directory="outdir" format="fasta" visible="false"/>
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139 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fa$" directory="outdir" format="fasta" visible="false"/>
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140 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt$" directory="outdir" format="txt" visible="false"/>
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141 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.clstr$" directory="outdir" format="txt" visible="false"/>
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142 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.gml$" directory="outdir" format="txt" visible="false"/>
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143 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.csv$" directory="outdir" format="csv" visible="false"/>
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144 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.Rtab$" directory="outdir" format="tabular" visible="false"/>
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145 <filter>( advanced['adv_options_selector'] != 'set' ) or ( advanced['adv_options_selector'] == 'set' and advanced['gene_alignment_option']['alignment'] == 'None' )</filter>
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146 </collection>
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147
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148 <!--Panaroo advance alignment outputs -->
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149 <collection name="output_pangenome" type="list" label="${tool.name} on ${on_string}: Pangenome alignment output">
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150 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.clstr$" directory="outdir" format="txt" visible="false"/>
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151 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt$" directory="outdir" format="txt" visible="false"/>
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152 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.gml$" directory="outdir" format="txt" visible="false"/>
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153 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.Rtab$" directory="outdir" format="tabular" visible="false"/>
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154 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.csv$" directory="outdir" format="csv" visible="false"/>
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155 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta$" directory="outdir" format="fasta" visible="false"/>
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156 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fa$" directory="outdir" format="fasta" visible="false"/>
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157 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.aln$" directory="outdir" format="fasta" visible="false"/>
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158 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.embl$" directory="outdir" format="embl" visible="false"/>
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159 <filter>advanced['adv_options_selector'] == 'set' and advanced['gene_alignment_option']['alignment'] != 'None' </filter>
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160 </collection>
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161
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162 <!--Pan Genome Aligned FASTA -->
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163 <collection name="output_pangenome_fasta" type="list" label="${tool.name} on ${on_string}: Pangenome Alignment Gene Sequences">
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164 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fas$" directory="outdir/aligned_gene_sequences" format="fasta" visible="false"/>
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165 <filter>advanced['adv_options_selector'] == 'set' and advanced['gene_alignment_option']['alignment'] != 'None'</filter>
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166 </collection>
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167
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168 <!--Panaroo log output -->
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169 <data name="log" format="txt" label="${tool.name} on ${on_string}: Panaroo Log">
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170 <filter>log_out</filter>
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171 </data>
0
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172 </outputs>
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173 <tests>
1
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174 <!-- Test 1 : Testing Panaroo with default parameters -->
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175 <test expect_num_outputs="2">
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176 <param name="mode" value="strict"/>
0
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177 <param name="gen_code" value="11"/>
1
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178 <param name="log_out" value="yes"/>
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179 <conditional name="advanced">
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180 <param name="adv_options_selector" value="do_not_set"/>
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181 </conditional>
0
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182 <param name="gff_input_collection">
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183 <collection type="list">
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184 <element name="10_small.gff" value="10_small.gff"/>
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185 <element name="11_small.gff" value="11_small.gff"/>
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186 </collection>
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187 </param>
1
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188 <output_collection name="output" count="13" type="list">
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189 <element name="combined_DNA_CDS" ftype="fasta">
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190 <assert_contents>
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191 <has_n_lines n="18206"/>
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192 </assert_contents>
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193 </element>
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194 <element name="combined_protein_CDS" ftype="fasta">
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195 <assert_contents>
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196 <has_n_lines n="7048"/>
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197 </assert_contents>
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198 </element>
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199 <element name="combined_protein_cdhit_out" ftype="fasta">
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200 <assert_contents>
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201 <has_n_lines n="5119"/>
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202 </assert_contents>
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203 </element>
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204 <element name="pan_genome_reference" ftype="fasta">
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205 <assert_contents>
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206 <has_n_lines n="5055"/>
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207 </assert_contents>
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208 </element>
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209 <element name="summary_statistics" ftype="txt">
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210 <assert_contents>
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211 <has_line line="Core genes&#009;(99% &#60;= strains &#60;= 100%)&#009;251"/>
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212 <has_line line="Total genes&#009;(0% &#60;= strains &#60;= 100%)&#009;251"/>
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213 </assert_contents>
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214 </element>
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215 <element name="gene_data" ftype="csv">
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216 <assert_contents>
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217 <has_text text="KPLBOJCC_00001"/>
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218 <has_text text="NCFNLLIC_00549"/>
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219 </assert_contents>
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220 </element>
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221 <element name="gene_presence_absence" ftype="csv">
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222 <assert_contents>
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223 <has_text text="dcd"/>
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224 <has_text text="trmB"/>
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225 <has_text text="betI_1"/>
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226 </assert_contents>
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227 </element>
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228 <element name="gene_presence_absence_roary" ftype="csv">
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229 <assert_contents>
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230 <has_text text="kstR2_1"/>
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231 <has_text text="ybgJ"/>
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232 </assert_contents>
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233 </element>
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234 <element name="struct_presence_absence" ftype="tabular">
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235 <assert_contents>
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236 <has_line_matching expression="Gene\s+10_small\s+11_small"/>
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237 </assert_contents>
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238 </element>
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239 </output_collection>
0
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240 <output name="log">
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241 <assert_contents>
1
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242 <has_text text="total seq: 979"/>
0
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243 </assert_contents>
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244 </output>
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galaxy-australia
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245 </test>
1
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246
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247 <!-- Test 2 : Testing Panaroo with Advanced filtering option along with Alignment turned off -->
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248 <test expect_num_outputs="2">
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249 <param name="gen_code" value="11"/>
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250 <param name="mode" value="strict"/>
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251 <param name="log_out" value="yes"/>
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252 <conditional name="advanced">
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253 <param name="adv_options_selector" value="set"/>
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254 <section name="gene_alignment_option">
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255 <param name="alignment" value="None"/>
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256 </section>
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257 </conditional>
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258 <param name="gff_input_collection">
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259 <collection type="list">
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260 <element name="10_small.gff" value="10_small.gff"/>
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261 <element name="11_small.gff" value="11_small.gff"/>
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262 </collection>
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263 </param>
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264 <output_collection name="output" count="13" type="list">
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265 <element name="combined_DNA_CDS" ftype="fasta">
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266 <assert_contents>
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267 <has_n_lines n="18206"/>
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268 </assert_contents>
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269 </element>
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270 <element name="combined_protein_CDS" ftype="fasta">
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271 <assert_contents>
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272 <has_n_lines n="7048"/>
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273 </assert_contents>
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274 </element>
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275 <element name="combined_protein_cdhit_out" ftype="fasta">
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276 <assert_contents>
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277 <has_n_lines n="5119"/>
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278 </assert_contents>
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279 </element>
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280 <element name="pan_genome_reference" ftype="fasta">
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281 <assert_contents>
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282 <has_n_lines n="13120"/>
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283 </assert_contents>
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284 </element>
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285 <element name="summary_statistics" ftype="txt">
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286 <assert_contents>
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287 <has_line line="Core genes&#009;(99% &#60;= strains &#60;= 100%)&#009;251"/>
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288 <has_line line="Shell genes&#009;(15% &#60;= strains &#60; 95%)&#009;475"/>
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289 <has_line line="Total genes&#009;(0% &#60;= strains &#60;= 100%)&#009;726"/>
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290 </assert_contents>
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291 </element>
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292 <element name="gene_data" ftype="csv">
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293 <assert_contents>
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294 <has_n_lines n="980"/>
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295 <has_n_columns sep="," n="8"/>
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296 <has_text text="KPLBOJCC_00003"/>
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297 <has_text text="NCFNLLIC_00003"/>
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298 </assert_contents>
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299 </element>
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300 <element name="gene_presence_absence" ftype="csv">
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301 <assert_contents>
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302 <has_text text="recB"/>
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303 <has_text text="recC"/>
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304 <has_text text="rpoB"/>
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305 </assert_contents>
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306 </element>
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307 <element name="gene_presence_absence_roary" ftype="csv">
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308 <assert_contents>
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309 <has_text text="ctpI_2"/>
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310 <has_text text="amiD_1"/>
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311 </assert_contents>
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312 </element>
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313 <element name="struct_presence_absence" ftype="tabular">
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314 <assert_contents>
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315 <has_line_matching expression="Gene\s+10_small\s+11_small"/>
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316 </assert_contents>
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317 </element>
0
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galaxy-australia
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318 </output_collection>
1
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319 <output name="log">
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320 <assert_contents>
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321 <has_text text="total seq: 979"/>
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322 </assert_contents>
0
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galaxy-australia
parents:
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323 </output>
1
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324 </test>
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325 <!-- Test 3 : Testing Panaroo with Advanced Filtering options along with MAFFT core alignment -->
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326 <test expect_num_outputs="3">
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327 <param name="gen_code" value="11"/>
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328 <param name="mode" value="strict"/>
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329 <param name="log_out" value="yes"/>
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330 <conditional name="advanced">
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331 <param name="adv_options_selector" value="set"/>
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332 <section name="gene_alignment_option">
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333 <param name="alignment" value="core"/>
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334 <param name="aligner" value="mafft"/>
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335 </section>
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336 </conditional>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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337 <param name="gff_input_collection">
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338 <collection type="list">
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diff changeset
339 <element name="10_small.gff" value="10_small.gff"/>
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diff changeset
340 <element name="11_small.gff" value="11_small.gff"/>
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diff changeset
341 </collection>
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342 </param>
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343 <output_collection name="output_pangenome" count="18" type="list">
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diff changeset
344 <element name="summary_statistics" ftype="txt">
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iuc
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diff changeset
345 <assert_contents>
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346 <has_line line="Core genes&#009;(99% &#60;= strains &#60;= 100%)&#009;251"/>
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diff changeset
347 <has_line line="Shell genes&#009;(15% &#60;= strains &#60; 95%)&#009;475"/>
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diff changeset
348 <has_line line="Total genes&#009;(0% &#60;= strains &#60;= 100%)&#009;726"/>
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iuc
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diff changeset
349 </assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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diff changeset
350 </element>
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diff changeset
351 <element name="alignment_entropy" ftype="csv">
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iuc
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diff changeset
352 <assert_contents>
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353 <has_text text="stf0.aln,0.0"/>
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354 <has_text text="bglB.aln,0.0"/>
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iuc
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diff changeset
355 </assert_contents>
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iuc
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diff changeset
356 </element>
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iuc
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diff changeset
357 <element name="combined_DNA_CDS" ftype="fasta">
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iuc
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diff changeset
358 <assert_contents>
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359 <has_n_lines n="18206"/>
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iuc
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diff changeset
360 </assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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diff changeset
361 </element>
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iuc
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diff changeset
362 <element name="combined_protein_cdhit_out" ftype="fasta">
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iuc
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diff changeset
363 <assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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364 <has_n_lines n="5119"/>
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iuc
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diff changeset
365 </assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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diff changeset
366 </element>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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diff changeset
367 <element name="combined_protein_CDS" ftype="fasta">
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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diff changeset
368 <assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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369 <has_n_lines n="7048"/>
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iuc
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diff changeset
370 </assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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diff changeset
371 </element>
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diff changeset
372 <element name="struct_presence_absence" ftype="tabular">
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iuc
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diff changeset
373 <assert_contents>
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374 <has_line_matching expression="Gene\s+10_small\s+11_small"/>
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iuc
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diff changeset
375 </assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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diff changeset
376 </element>
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diff changeset
377 <element name="gene_data" ftype="csv">
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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diff changeset
378 <assert_contents>
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379 <has_n_lines n="980"/>
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diff changeset
380 <has_n_columns sep="," n="8"/>
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381 <has_text text="KPLBOJCC_00003"/>
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382 <has_text text="NCFNLLIC_00003"/>
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diff changeset
383 </assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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diff changeset
384 </element>
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diff changeset
385 <element name="pan_genome_reference" ftype="fasta">
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iuc
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diff changeset
386 <assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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387 <has_n_lines n="13120"/>
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diff changeset
388 </assert_contents>
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diff changeset
389 </element>
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diff changeset
390 <element name="gene_presence_absence" ftype="csv">
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diff changeset
391 <assert_contents>
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392 <has_text text="recB"/>
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393 <has_text text="recC"/>
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394 <has_text text="rpoB"/>
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diff changeset
395 </assert_contents>
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396 </element>
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397 <element name="gene_presence_absence_roary" ftype="csv">
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diff changeset
398 <assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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399 <has_text text="ctpI_2"/>
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400 <has_text text="amiD_1"/>
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iuc
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diff changeset
401 </assert_contents>
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diff changeset
402 </element>
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diff changeset
403 <element name="core_gene_alignment_filtered" ftype="fasta">
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iuc
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diff changeset
404 <assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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405 <has_size value="569962" delta="1000"/>
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diff changeset
406 </assert_contents>
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diff changeset
407 </element>
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diff changeset
408 <element name="core_gene_alignment" ftype="fasta">
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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diff changeset
409 <assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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410 <has_size value="569962" delta="1000"/>
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iuc
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diff changeset
411 </assert_contents>
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diff changeset
412 </element>
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diff changeset
413 <element name="core_alignment_header" ftype="embl">
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iuc
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diff changeset
414 <assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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diff changeset
415 <has_text text="ID Genome standard; DNA; PRO; 1234 BP."/>
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416 <has_text text="hisB_1.aln"/>
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iuc
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diff changeset
417 </assert_contents>
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diff changeset
418 </element>
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diff changeset
419 <element name="core_alignment_filtered_header" ftype="embl">
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diff changeset
420 <assert_contents>
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421 <has_n_lines n="760" delta="10"/>
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iuc
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diff changeset
422 </assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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diff changeset
423 </element>
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424 </output_collection>
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diff changeset
425 <output_collection name="output_pangenome_fasta" count="251"/>
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parents: 0
diff changeset
426 <output name="log">
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
parents: 0
diff changeset
427 <assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
parents: 0
diff changeset
428 <has_text text="total seq: 979"/>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
parents: 0
diff changeset
429 </assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
parents: 0
diff changeset
430 </output>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
parents: 0
diff changeset
431 </test>
0
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
432 </tests>
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
433 <help><![CDATA[
1
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
parents: 0
diff changeset
434 Panaroo_ is a pangenome analysis tool specifically designed to analyze bacterial genomes. Panaroo builds a full graphical representation of the pangenome, where nodes are clusters of orthologous genes (COGs) and two nodes are connected by an edge if they are adjacent on a contig in any sample from the population. Using this graphical representation, Panaroo corrects for errors introduced during annotation by collapsing diverse gene families, filtering contamination, merging fragmented gene segments and refinding missing genes.
0
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
435
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
436 **INPUTS**
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
437
1
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
parents: 0
diff changeset
438 - A list of gff3 files (from Prokka) in a collection.
0
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
439
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
440 **OUTPUTS**
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
441
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
442 - combined_protein_cdhit_out.txt
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
443 - combined_protein_cdhit_out.txt.clstr
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
444 - pre_filt_graph.gml
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
445 - gene_data.csv
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
446 - combined_protein_CDS.fasta
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
447 - combined_DNA_CDS.fasta
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
448 - gene_presence_absence_rtab.Rtab
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
449 - gene_presence_absence_roary.csv
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
450 - gene_presence_absence.csv
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
451 - summary_statistics.txt
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
452 - pan_genome_reference.fa
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
453 - struct_presence_absence.Rtab
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
454 - final_graph.gml
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
455
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
456 **OUTPUTS with Advance parameters**
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
457
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
458 - combined_protein_cdhit_out.txt
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
459 - combined_protein_cdhit_out.txt.clstr
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
460 - pre_filt_graph.gml
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
461 - gene_data.csv
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
462 - combined_protein_CDS.fasta
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
463 - combined_DNA_CDS.fasta
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
464 - gene_presence_absence_rtab.Rtab
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
465 - gene_presence_absence_roary.csv
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
466 - gene_presence_absence.csv
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
467 - summary_statistics.txt
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
468 - pan_genome_reference.fa
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
469 - struct_presence_absence.Rtab
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
470 - final_graph.gml
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
471 - core_gene_alignment
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
472 - core_gene_alignment_filtered
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
473 - core_alignment_filtered_header
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
474 - core_alignment_header
1
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
parents: 0
diff changeset
475 - a collection of Pangenome Aligned Fasta files
0
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
476
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
477 .. _Panaroo: https://gthlab.au/panaroo/#/gettingstarted/quickstart
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
478
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
479 ]]></help>
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
480 <citations>
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
481 <citation type="doi">10.1186/s13059-020-02090-4</citation>
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
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diff changeset
482 </citations>
1
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
parents: 0
diff changeset
483 </tool>