Mercurial > repos > iuc > checkm_tree_qa

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 97fbd010c5406d4980d64b320f25f4716aea2fc9
author iuc
date Tue, 17 Jun 2025 12:55:24 +0000
parents df9e3191e6da
children
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df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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1 <tool id="checkm_tree_qa" name="CheckM tree_qa" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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2 <description>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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3 Assess phylogenetic markers in the genome tree
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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4 </description>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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5 <macros>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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6 <import>macros.xml</import>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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7 <xml name="concatenated_tre">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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8 <param name="concatenated_tre" type="data" format="phyloxml" label="Concatenated tree"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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9 </xml>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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10 </macros>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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11 <expand macro="biotools"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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12 <expand macro="requirements"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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13 <expand macro="version"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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14 <command detect_errors="exit_code"><![CDATA[
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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15 @HMM_MARKER_STATS_INPUTS@
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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16 mkdir 'inputs/storage/tree/' &&
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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17 #if $output.out_format != '5'
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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18 ln -s '$output.concatenated_tre' 'inputs/storage/tree/concatenated.tre' &&
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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19 #else
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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20 ln -s '$output.concatenated_fasta' 'inputs/storage/tree/concatenated.fasta' &&
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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21 #end if
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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22
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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23 checkm tree_qa
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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24 'inputs'
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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25 --out_format $output.out_format
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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26 --tab_table
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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27 --file 'output_file'
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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28 ]]></command>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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29 <inputs>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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30 <expand macro="hmm_marker_stats_inputs"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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31 <conditional name="output">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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32 <param argument="--out_format" type="select" label="Desired output">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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33 <option value="1">Brief summary of genome tree placement</option>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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34 <option value="2">Detailed summary of genome tree placement including lineage-specific statistics</option>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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35 <option value="3">Genome tree in Newick format decorated with IMG genome ids</option>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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36 <option value="4">Genome tree in Newick format decorated with taxonomy strings</option>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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37 <option value="5">Multiple sequence alignment of reference genomes and bins</option>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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38 </param>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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39 <when value="1">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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40 <expand macro="concatenated_tre"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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41 </when>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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42 <when value="2">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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43 <expand macro="concatenated_tre"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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44 </when>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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45 <when value="3">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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46 <expand macro="concatenated_tre"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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47 </when>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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48 <when value="4">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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49 <expand macro="concatenated_tre"/>
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50 </when>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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51 <when value="5">
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52 <param name="concatenated_fasta" type="data" format="phyloxml" label="Concatenated masked sequences"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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53 </when>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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54 </conditional>
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55 </inputs>
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56 <outputs>
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57 <data name="output_f1" format="tabular" from_work_dir="output_file" label="${tool.name} on ${on_string}: Summary of genome tree placement">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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58 <filter>output['out_format']=="1"</filter>
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59 </data>
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60 <data name="output_f2" format="tabular" from_work_dir="output_file" label="${tool.name} on ${on_string}: Summary of genome tree placement including lineage-specific statistics">
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61 <filter>output['out_format']=="2"</filter>
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62 </data>
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63 <data name="output_f3" format="newick" from_work_dir="output_file" label="${tool.name} on ${on_string}: Genome tree decorated with IMG genome ids">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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64 <filter>output['out_format']=="3"</filter>
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65 </data>
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66 <data name="output_f4" format="newick" from_work_dir="output_file" label="${tool.name} on ${on_string}: Genome tree decorated with taxonomy strings">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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67 <filter>output['out_format']=="4"</filter>
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68 </data>
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69 <data name="output_f5" format="tabular" from_work_dir="output_file" label="${tool.name} on ${on_string}: Multiple sequence alignment of reference genomes and bins">
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70 <filter>output['out_format']=="5"</filter>
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71 </data>
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72 </outputs>
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73 <tests>
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74 <test expect_num_outputs="1">
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75 <param name="phylo_hmm_info" ftype="zip" value="phylo_hmm_info.pkl.gz"/>
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76 <param name="bin_stats_tree" ftype="tabular" value="bin_stats.tree.tsv"/>
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77 <param name="hmmer_tree">
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78 <collection type="list">
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79 <element name="637000110" ftype="txt" value="hmmer.tree.txt"/>
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80 </collection>
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81 </param>
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82 <conditional name="output">
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83 <param name="out_format" value="1"/>
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84 <param name="concatenated_tre" ftype="phyloxml" value="concatenated.tre"/>
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85 </conditional>
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86 <output name="output_f1" ftype="tabular">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
87 <assert_contents>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
88 <has_text text="637000110"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
89 <has_text text="k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
90 <has_text text="# unique markers"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
91 </assert_contents>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
92 </output>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
93 </test>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
94 <test expect_num_outputs="1">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
95 <param name="phylo_hmm_info" ftype="zip" value="phylo_hmm_info.pkl.gz"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
96 <param name="bin_stats_tree" ftype="tabular" value="bin_stats.tree.tsv"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
97 <param name="hmmer_tree">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
98 <collection type="list">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
99 <element name="637000110" ftype="txt" value="hmmer.tree.txt"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
100 </collection>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
101 </param>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
102 <conditional name="output">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
103 <param name="out_format" value="2"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
104 <param name="concatenated_tre" ftype="phyloxml" value="concatenated.tre"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
105 </conditional>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
106 <output name="output_f2" ftype="tabular">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
107 <assert_contents>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
108 <has_text text="637000110"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
109 <has_text text="# unique markers (of 43)"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
110 <has_text text="UID5220"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
111 </assert_contents>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
112 </output>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
113 </test>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
114 <test expect_num_outputs="1">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
115 <param name="phylo_hmm_info" ftype="zip" value="phylo_hmm_info.pkl.gz"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
116 <param name="bin_stats_tree" ftype="tabular" value="bin_stats.tree.tsv"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
117 <param name="hmmer_tree">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
118 <collection type="list">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
119 <element name="IMG_646564547" ftype="txt" value="hmmer.tree.txt"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
120 </collection>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
121 </param>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
122 <conditional name="output">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
123 <param name="out_format" value="3"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
124 <param name="concatenated_tre" ftype="phyloxml" value="concatenated.tre"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
125 </conditional>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
126 <output name="output_f3" ftype="newick">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
127 <assert_contents>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
128 <has_text text="IMG_646564547"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
129 <has_text text="UID7|f__Methanocaldococcaceae"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
130 <has_text text="f__Archaeoglobaceae"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
131 </assert_contents>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
132 </output>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
133 </test>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
134 <test expect_num_outputs="1">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
135 <param name="phylo_hmm_info" ftype="zip" value="phylo_hmm_info.pkl.gz"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
136 <param name="bin_stats_tree" ftype="tabular" value="bin_stats.tree.tsv"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
137 <param name="hmmer_tree">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
138 <collection type="list">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
139 <element name="637000110" ftype="txt" value="hmmer.tree.txt"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
140 </collection>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
141 </param>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
142 <conditional name="output">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
143 <param name="out_format" value="4"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
144 <param name="concatenated_tre" ftype="phyloxml" value="concatenated.tre"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
145 </conditional>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
146 <output name="output_f4" ftype="newick">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
147 <assert_contents>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
148 <has_text text="IMG_646564547"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
149 <has_text text="k__Archaea;p__Euryarchaeota"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
150 </assert_contents>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
151 </output>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
152 </test>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
153 <test expect_num_outputs="1">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
154 <param name="phylo_hmm_info" ftype="zip" value="phylo_hmm_info.pkl.gz"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
155 <param name="bin_stats_tree" ftype="tabular" value="bin_stats.tree.tsv"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
156 <param name="hmmer_tree">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
157 <collection type="list">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
158 <element name="637000110" ftype="txt" value="hmmer.tree.txt"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
159 </collection>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
160 </param>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
161 <conditional name="output">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
162 <param name="out_format" value="5"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
163 <param name="concatenated_fasta" ftype="fasta" value="concatenated.fasta"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
164 </conditional>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
165 <output name="output_f5" ftype="tabular">
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
166 <assert_contents>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
167 <has_text text=">637000110"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
168 <has_text text="-TVNQLVR"/>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
169 </assert_contents>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
170 </output>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
171 </test>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
172 </tests>
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
173 <help><![CDATA[
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
174 @HELP_HEADER@
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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176 This command assesses phylogenetic markers in the genome tree
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177
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178 Inputs
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179 ======
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180
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181
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182 Outputs
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183 =======
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184
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185 Output in function of selection output format
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186
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187 1. brief summary of genome tree placement indicating the number of unique phylogenetically informative markers found, the number of markers found multiple times, and a taxon string indicating the placement of each bin within the genome tree
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188 2. detailed summary of genome tree placement giving a more detailed indication of where each bin is within the genome tree, general characteristics about each bin (e.g., GC, genome size, coding density), and general characteristics about all reference genomes descendant from the parental node of each bin (e.g., mean and standard deviation of GC)
df9e3191e6da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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189 3. genome tree in Newick format decorated with IMG genome ids which can be used to examine the phylogenetic neighbours of each bin
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190 4. genome tree in Newick format decorated with taxonomy strings which can be used to examine the phylogenetic neighbours of each bin
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191 5. multiple sequence alignment of reference genomes and bins which can be used to infer a de novo genome tree
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192
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193
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194 ]]></help>
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195 <expand macro="citations"/>
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196 </tool>