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annotate panaroo.xml @ 2:b05be6316263 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo commit 95eb601ee5e08ebcca551bd949b83e0b85718df8
author iuc
date Tue, 20 Jan 2026 13:23:28 +0000
parents b6a78d286482
children
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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>
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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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
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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
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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/$identifier' &&
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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17 #end for
0
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18
1
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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19 panaroo
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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20 --clean-mode '$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
iuc
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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'
2
b05be6316263 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo commit 95eb601ee5e08ebcca551bd949b83e0b85718df8
iuc
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31 --family_len_dif_percent '$advanced.matching_option.family_len_dif_percent'
1
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32 $advanced.matching_option.merge_paralogs
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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33 --search_radius '$advanced.refind_option.search_radius'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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34 --refind_prop_match '$advanced.refind_option.refind_prop_match'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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35 --refind-mode '$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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36 --min_trailing_support '$advanced.graph_correction_option.min_trailing_support'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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37 --trailing_recursive '$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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38 --edge_support_threshold '$advanced.graph_correction_option.edge_support_threshold'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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39 --remove_by_consensus '$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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40 --high_var_flag '$advanced.graph_correction_option.high_var_flag'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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41 --min_edge_support_sv '$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
iuc
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42 $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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43 $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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44 #if $advanced.gene_alignment_option.alignment != 'None'
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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45 --alignment '$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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46 --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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47 #end if
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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48 #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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49 --core_subset $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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50 #end if
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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51 #if $advanced.gene_alignment_option.core_entropy_filter
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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52 --core_entropy_filter $advanced.gene_alignment_option.core_entropy_filter
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53 #end if
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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54 #end if
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55 -i $input_directory/*.gff
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56 -o outdir
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57 -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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58 #if $log_out
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59 2>&1 | tee '$log'
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60 #end if
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61 && mv outdir/gene_presence_absence.Rtab outdir/gene_presence_absence_rtab.Rtab &&
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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62 mv outdir/combined_protein_cdhit_out.txt outdir/combined_protein_cdhit_out.fa
0
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63 ]]></command>
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64 <inputs>
1
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65 <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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66 <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.">
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="strict">Strict</option>
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68 <option value="moderate">Moderate</option>
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69 <option value="sensitive">Sensitive</option>
0
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70 </param>
1
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71 <param name="gen_code" type="select" label="The Codon table used for translation" help="Default: 11.Bacteria and Archaea">
0
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72 <expand macro="genetic_code"/>
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73 </param>
1
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74 <param name="log_out" type="boolean" label="Output log file?" truevalue="yes" falsevalue="no"/>
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75 <conditional name="advanced">
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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76 <param name="adv_options_selector" type="select" label="Set Advanced Options?" help="Fine Tuning of Panaroo algorithmic parameters">
0
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77 <option value="set">Set</option>
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
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78 <option value="do_not_set" selected="True">Do not set</option>
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79 </param>
1
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80 <when value="set">
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81 <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."/>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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82
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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83 <!--Options for Matching-->
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84 <section name="matching_option" title="Matching" expanded="false">
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85 <param argument="--threshold" type="float" value="0.98" label="Sequence identity threshold" help="default: 0.98"/>
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86 <param argument="--family_threshold" type="float" value="0.7" label="Protein family sequence identity threshold" help="default: 0.7"/>
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87 <param argument="--len_dif_percent" type="float" value="0.98" label="Length difference cutoff" help="default: 0.98"/>
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88 <param argument="--family_len_dif_percent" type="float" value="0.0" label="Length difference cutoff at the gene family level" help="default: 0.0"/>
1
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89 <param argument="--merge-paralogs" type="boolean" truevalue="--merge_paralogs" falsevalue="" label="Merge Paralogs"/>
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90 </section>
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91
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92 <!--Options for Refind-->
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93 <section name="refind_option" title="Refind" expanded="false">
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94 <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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95 <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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96 <param argument="--refind_mode" type="select" label="Refind Mode" help="Set the stringency mode at which to re-find genes">
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97 <option value="default" selected="True">Default</option>
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98 <option value="strict">Strict</option>
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99 <option value="off">Off</option>
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100 </param>
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101 </section>
0
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102
1
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103 <!--Graph Correction-->
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104 <section name="graph_correction_option" title="Graph Correction" expanded="false">
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105 <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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106 <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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107 <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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108 <param argument="--len_outlier_proportion" type="float" value="0.01" label="Length outlier support proportion" help="--length_outlier_support_proportion"/>
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109 <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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110 <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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111 <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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112 <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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113 <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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114 </section>
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115
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116 <!--Gene Alignment-->
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117 <section name="gene_alignment_option" title="Gene Alignment" expanded="false">
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118 <param argument="--alignment" type="select" label="Output alignments of core genes or all genes.">
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119 <option value="None" selected="True">None</option>
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120 <option value="core">Core genome alignment</option>
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121 <option value="pan">Pan-genome alignment</option>
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122 </param>
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123 <param argument="--aligner" type="select" label="Specify an aligner" help="--aligner [mafft|prank|clustal][default: mafft]">
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124 <option value="mafft" selected="True">MAFFT</option>
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125 <option value="prank">PRANK</option>
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126 <option value="clustal">Clustal</option>
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127 </param>
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128 <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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129 <param argument="--core_threshold" type="float" value="0.95" label="Core Threshold" help="Core-genome sample threshold"/>
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130 <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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131 <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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132 </section>
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133 </when>
0
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134 <when value="do_not_set"/>
1
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135 </conditional>
0
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136 </inputs>
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137 <outputs>
1
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138 <!--Panaroo default outputs -->
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139 <collection name="output" type="list" label="${tool.name} on ${on_string}: Pangenome default output">
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140 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta$" directory="outdir" format="fasta" visible="false"/>
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141 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fa$" directory="outdir" format="fasta" visible="false"/>
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142 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt$" directory="outdir" format="txt" visible="false"/>
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143 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.clstr$" directory="outdir" format="txt" visible="false"/>
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144 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.gml$" directory="outdir" format="txt" visible="false"/>
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145 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.csv$" directory="outdir" format="csv" visible="false"/>
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146 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.Rtab$" directory="outdir" format="tabular" visible="false"/>
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147 <filter>( advanced['adv_options_selector'] != 'set' ) or ( advanced['adv_options_selector'] == 'set' and advanced['gene_alignment_option']['alignment'] == 'None' )</filter>
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148 </collection>
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149
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150 <!--Panaroo advance alignment outputs -->
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151 <collection name="output_pangenome" type="list" label="${tool.name} on ${on_string}: Pangenome alignment output">
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152 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.clstr$" directory="outdir" format="txt" visible="false"/>
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153 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt$" directory="outdir" format="txt" visible="false"/>
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154 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.gml$" directory="outdir" format="txt" visible="false"/>
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155 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.Rtab$" directory="outdir" format="tabular" visible="false"/>
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156 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.csv$" directory="outdir" format="csv" visible="false"/>
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157 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta$" directory="outdir" format="fasta" visible="false"/>
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158 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fa$" directory="outdir" format="fasta" visible="false"/>
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159 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.aln$" directory="outdir" format="fasta" visible="false"/>
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160 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.embl$" directory="outdir" format="embl" visible="false"/>
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161 <filter>advanced['adv_options_selector'] == 'set' and advanced['gene_alignment_option']['alignment'] != 'None' </filter>
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162 </collection>
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163
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164 <!--Pan Genome Aligned FASTA -->
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165 <collection name="output_pangenome_fasta" type="list" label="${tool.name} on ${on_string}: Pangenome Alignment Gene Sequences">
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166 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fas$" directory="outdir/aligned_gene_sequences" format="fasta" visible="false"/>
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167 <filter>advanced['adv_options_selector'] == 'set' and advanced['gene_alignment_option']['alignment'] != 'None'</filter>
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168 </collection>
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169
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170 <!--Panaroo log output -->
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171 <data name="log" format="txt" label="${tool.name} on ${on_string}: Panaroo Log">
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172 <filter>log_out</filter>
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173 </data>
0
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174 </outputs>
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175 <tests>
1
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176 <!-- Test 1 : Testing Panaroo with default parameters -->
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177 <test expect_num_outputs="2">
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178 <param name="mode" value="strict"/>
0
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galaxy-australia
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179 <param name="gen_code" value="11"/>
1
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180 <param name="log_out" value="yes"/>
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181 <conditional name="advanced">
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182 <param name="adv_options_selector" value="do_not_set"/>
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183 </conditional>
0
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galaxy-australia
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184 <param name="gff_input_collection">
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galaxy-australia
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185 <collection type="list">
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galaxy-australia
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186 <element name="10_small.gff" value="10_small.gff"/>
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galaxy-australia
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187 <element name="11_small.gff" value="11_small.gff"/>
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galaxy-australia
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188 </collection>
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189 </param>
1
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190 <output_collection name="output" count="13" type="list">
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191 <element name="combined_DNA_CDS" ftype="fasta">
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192 <assert_contents>
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193 <has_n_lines n="18206"/>
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194 </assert_contents>
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195 </element>
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196 <element name="combined_protein_CDS" ftype="fasta">
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197 <assert_contents>
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198 <has_n_lines n="7048"/>
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199 </assert_contents>
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200 </element>
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201 <element name="combined_protein_cdhit_out" ftype="fasta">
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202 <assert_contents>
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iuc
parents: 0
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203 <has_n_lines n="5119"/>
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204 </assert_contents>
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205 </element>
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206 <element name="pan_genome_reference" ftype="fasta">
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207 <assert_contents>
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208 <has_n_lines n="5055"/>
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209 </assert_contents>
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210 </element>
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211 <element name="summary_statistics" ftype="txt">
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212 <assert_contents>
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213 <has_line line="Core genes&#009;(99% &#60;= strains &#60;= 100%)&#009;251"/>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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214 <has_line line="Total genes&#009;(0% &#60;= strains &#60;= 100%)&#009;251"/>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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215 </assert_contents>
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216 </element>
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217 <element name="gene_data" ftype="csv">
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218 <assert_contents>
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219 <has_text text="KPLBOJCC_00001"/>
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220 <has_text text="NCFNLLIC_00549"/>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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221 </assert_contents>
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222 </element>
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223 <element name="gene_presence_absence" ftype="csv">
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224 <assert_contents>
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225 <has_text text="dcd"/>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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226 <has_text text="trmB"/>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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227 <has_text text="betI_1"/>
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228 </assert_contents>
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229 </element>
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230 <element name="gene_presence_absence_roary" ftype="csv">
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231 <assert_contents>
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iuc
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232 <has_text text="kstR2_1"/>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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233 <has_text text="ybgJ"/>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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234 </assert_contents>
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iuc
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235 </element>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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236 <element name="struct_presence_absence" ftype="tabular">
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237 <assert_contents>
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238 <has_line_matching expression="Gene\s+10_small\s+11_small"/>
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iuc
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239 </assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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240 </element>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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241 </output_collection>
0
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galaxy-australia
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242 <output name="log">
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galaxy-australia
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243 <assert_contents>
1
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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244 <has_text text="total seq: 979"/>
0
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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245 </assert_contents>
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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246 </output>
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247 </test>
1
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248
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249 <!-- Test 2 : Testing Panaroo with Advanced filtering option along with Alignment turned off -->
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250 <test expect_num_outputs="2">
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251 <param name="gen_code" value="11"/>
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252 <param name="mode" value="strict"/>
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253 <param name="log_out" value="yes"/>
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254 <conditional name="advanced">
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255 <param name="adv_options_selector" value="set"/>
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256 <section name="gene_alignment_option">
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257 <param name="alignment" value="None"/>
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258 </section>
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259 </conditional>
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260 <param name="gff_input_collection">
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261 <collection type="list">
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262 <element name="10_small.gff" value="10_small.gff"/>
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263 <element name="11_small.gff" value="11_small.gff"/>
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264 </collection>
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265 </param>
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266 <output_collection name="output" count="13" type="list">
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267 <element name="combined_DNA_CDS" ftype="fasta">
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268 <assert_contents>
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269 <has_n_lines n="18206"/>
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270 </assert_contents>
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271 </element>
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272 <element name="combined_protein_CDS" ftype="fasta">
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273 <assert_contents>
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274 <has_n_lines n="7048"/>
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275 </assert_contents>
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276 </element>
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277 <element name="combined_protein_cdhit_out" ftype="fasta">
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278 <assert_contents>
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279 <has_n_lines n="5119"/>
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280 </assert_contents>
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281 </element>
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282 <element name="pan_genome_reference" ftype="fasta">
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283 <assert_contents>
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284 <has_n_lines n="13120"/>
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285 </assert_contents>
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286 </element>
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287 <element name="summary_statistics" ftype="txt">
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288 <assert_contents>
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289 <has_line line="Core genes&#009;(99% &#60;= strains &#60;= 100%)&#009;251"/>
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290 <has_line line="Shell genes&#009;(15% &#60;= strains &#60; 95%)&#009;475"/>
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291 <has_line line="Total genes&#009;(0% &#60;= strains &#60;= 100%)&#009;726"/>
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iuc
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292 </assert_contents>
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293 </element>
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294 <element name="gene_data" ftype="csv">
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295 <assert_contents>
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296 <has_n_lines n="980"/>
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297 <has_n_columns sep="," n="8"/>
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298 <has_text text="KPLBOJCC_00003"/>
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299 <has_text text="NCFNLLIC_00003"/>
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300 </assert_contents>
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301 </element>
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302 <element name="gene_presence_absence" ftype="csv">
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303 <assert_contents>
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304 <has_text text="recB"/>
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305 <has_text text="recC"/>
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306 <has_text text="rpoB"/>
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307 </assert_contents>
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308 </element>
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309 <element name="gene_presence_absence_roary" ftype="csv">
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310 <assert_contents>
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311 <has_text text="ctpI_2"/>
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312 <has_text text="amiD_1"/>
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313 </assert_contents>
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314 </element>
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315 <element name="struct_presence_absence" ftype="tabular">
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316 <assert_contents>
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317 <has_line_matching expression="Gene\s+10_small\s+11_small"/>
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318 </assert_contents>
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319 </element>
0
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galaxy-australia
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320 </output_collection>
1
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321 <output name="log">
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322 <assert_contents>
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323 <has_text text="total seq: 979"/>
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324 </assert_contents>
0
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galaxy-australia
parents:
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325 </output>
1
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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326 </test>
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327 <!-- Test 3 : Testing Panaroo with Advanced Filtering options along with MAFFT core alignment -->
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328 <test expect_num_outputs="3">
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329 <param name="gen_code" value="11"/>
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330 <param name="mode" value="strict"/>
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331 <param name="log_out" value="yes"/>
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332 <conditional name="advanced">
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333 <param name="adv_options_selector" value="set"/>
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334 <section name="gene_alignment_option">
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335 <param name="alignment" value="core"/>
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parents: 0
diff changeset
336 <param name="aligner" value="mafft"/>
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
337 </section>
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iuc
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diff changeset
338 </conditional>
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iuc
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diff changeset
339 <param name="gff_input_collection">
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340 <collection type="list">
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iuc
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diff changeset
341 <element name="10_small.gff" value="10_small.gff"/>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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diff changeset
342 <element name="11_small.gff" value="11_small.gff"/>
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iuc
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diff changeset
343 </collection>
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iuc
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diff changeset
344 </param>
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iuc
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diff changeset
345 <output_collection name="output_pangenome" count="18" type="list">
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iuc
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diff changeset
346 <element name="summary_statistics" ftype="txt">
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iuc
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diff changeset
347 <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
348 <has_line line="Core genes&#009;(99% &#60;= strains &#60;= 100%)&#009;251"/>
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iuc
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diff changeset
349 <has_line line="Shell genes&#009;(15% &#60;= strains &#60; 95%)&#009;475"/>
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iuc
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diff changeset
350 <has_line line="Total genes&#009;(0% &#60;= strains &#60;= 100%)&#009;726"/>
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
351 </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
352 </element>
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iuc
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diff changeset
353 <element name="alignment_entropy" ftype="csv">
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iuc
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diff changeset
354 <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
355 <has_text text="stf0.aln,0.0"/>
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diff changeset
356 <has_text text="bglB.aln,0.0"/>
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iuc
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diff changeset
357 </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
358 </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
359 <element name="combined_DNA_CDS" ftype="fasta">
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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 <has_n_lines n="18206"/>
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iuc
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diff changeset
362 </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
363 </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
364 <element name="combined_protein_cdhit_out" ftype="fasta">
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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
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366 <has_n_lines n="5119"/>
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iuc
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diff changeset
367 </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
368 </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
369 <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
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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371 <has_n_lines n="7048"/>
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iuc
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diff changeset
372 </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
373 </element>
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iuc
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diff changeset
374 <element name="struct_presence_absence" ftype="tabular">
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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
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376 <has_line_matching expression="Gene\s+10_small\s+11_small"/>
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
377 </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
378 </element>
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diff changeset
379 <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
380 <assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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381 <has_n_lines n="980"/>
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382 <has_n_columns sep="," n="8"/>
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383 <has_text text="KPLBOJCC_00003"/>
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384 <has_text text="NCFNLLIC_00003"/>
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diff changeset
385 </assert_contents>
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diff changeset
386 </element>
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diff changeset
387 <element name="pan_genome_reference" ftype="fasta">
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iuc
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diff changeset
388 <assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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389 <has_n_lines n="13120"/>
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iuc
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diff changeset
390 </assert_contents>
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diff changeset
391 </element>
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diff changeset
392 <element name="gene_presence_absence" ftype="csv">
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iuc
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diff changeset
393 <assert_contents>
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394 <has_text text="recB"/>
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395 <has_text text="recC"/>
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396 <has_text text="rpoB"/>
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iuc
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diff changeset
397 </assert_contents>
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iuc
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diff changeset
398 </element>
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diff changeset
399 <element name="gene_presence_absence_roary" ftype="csv">
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diff changeset
400 <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
401 <has_text text="ctpI_2"/>
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diff changeset
402 <has_text text="amiD_1"/>
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iuc
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diff changeset
403 </assert_contents>
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iuc
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diff changeset
404 </element>
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diff changeset
405 <element name="core_gene_alignment_filtered" ftype="fasta">
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iuc
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diff changeset
406 <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
407 <has_size value="569962" delta="1000"/>
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iuc
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diff changeset
408 </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
409 </element>
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iuc
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diff changeset
410 <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
iuc
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diff changeset
411 <assert_contents>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
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412 <has_size value="569962" delta="1000"/>
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iuc
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diff changeset
413 </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
414 </element>
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iuc
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diff changeset
415 <element name="core_alignment_header" ftype="embl">
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
416 <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
417 <has_text text="ID Genome standard; DNA; PRO; 1234 BP."/>
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418 <has_text text="hisB_1.aln"/>
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iuc
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diff changeset
419 </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
420 </element>
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iuc
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diff changeset
421 <element name="core_alignment_filtered_header" ftype="embl">
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
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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423 <has_n_lines n="760" delta="10"/>
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iuc
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diff changeset
424 </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
425 </element>
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iuc
parents: 0
diff changeset
426 </output_collection>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
parents: 0
diff changeset
427 <output_collection name="output_pangenome_fasta" count="251"/>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
parents: 0
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428 <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
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 <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
431 </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
432 </output>
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
parents: 0
diff changeset
433 </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
434 </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
435 <help><![CDATA[
1
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
parents: 0
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436 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
437
50483f852947 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 0abf1ced6a6d8f85ed4fc244de2bc337f889aca2-dirty
galaxy-australia
parents:
diff changeset
438 **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
439
1
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
parents: 0
diff changeset
440 - 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
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 **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
443
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 - 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
445 - 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
446 - 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
447 - 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
448 - 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
449 - 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
450 - 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
451 - 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
452 - 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
453 - 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
454 - 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
455 - 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
456 - 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
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 **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
459
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 - 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
461 - 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
462 - 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
463 - 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
464 - 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
465 - 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
466 - 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
467 - 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
468 - 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
469 - 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
470 - 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
471 - 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
472 - 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
473 - 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
474 - 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
475 - 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
476 - 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
477 - 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
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 .. _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
480
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 ]]></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
482 <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
483 <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
484 </citations>
1
b6a78d286482 planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/panaroo commit 23afccfad9fc0d2a4b91fd391f4847062fd98042
iuc
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485 </tool>