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annotate macros.xml @ 0:b39999cdbf21 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
author iuc
date Fri, 29 Jul 2022 20:38:36 +0000
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children 640400ad260d
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b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
1 <?xml version="1.0"?>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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2 <macros>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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3 <token name="@TOOL_VERSION@">1.2.0</token>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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4 <token name="@VERSION_SUFFIX@">0</token>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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5 <token name="@PROFILE@">21.01</token>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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6 <xml name="biotools">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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7 <xrefs>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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8 <xref type="bio.tools">checkm</xref>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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9 </xrefs>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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10 </xml>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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11 <xml name="requirements">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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12 <requirements>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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13 <requirement type="package" version="@TOOL_VERSION@">checkm-genome</requirement>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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14 <yield/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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15 </requirements>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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16 </xml>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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17 <xml name="bin_inputs">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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18 <conditional name="bins">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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19 <param name="select" type="select" label="Data structure for bins">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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20 <option value="collection">In collection</option>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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21 <option value="individual">In individual datasets</option>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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22 </param>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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23 <when value="collection">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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24 <param name="bins_coll" type="data_collection" collection_type="list" format="fasta" label="Bins"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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25 </when>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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26 <when value="individual">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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27 <param name="bins_ind" type="data" format="fasta" multiple="true" label="Bins"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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28 </when>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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29 </conditional>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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30 </xml>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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31 <token name="@BIN_INPUTS@"><![CDATA[
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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32 #import re
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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33 mkdir 'bins' &&
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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34 #if $bins.select == 'collection'
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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35 #for $b in $bins.bins_coll
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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36 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($b.element_identifier))
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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37 ln -s '$b.file_name' 'bins/${identifier}.fasta' &&
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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38 #end for
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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39 #else
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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40 #for $b in $bins.bins_ind
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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41 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($b.element_identifier))
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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42 ln -s '$b.file_name' 'bins/${identifier}.fasta' &&
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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43 #end for
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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44 #end if
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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45 ]]></token>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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46 <xml name="ali">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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47 <param argument="--ali" type="boolean" truevalue="--ali" falsevalue="" checked="false" label="Generate HMMER alignment file for each bin?" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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48 </xml>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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49 <xml name="nt">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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50 <param argument="--nt" type="boolean" truevalue="--nt" falsevalue="" checked="false" label="Generate nucleotide gene sequences for each bin?" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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51 </xml>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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52 <xml name="genes">
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53 <param argument="--genes" type="boolean" truevalue="--genes" falsevalue="" checked="false" label="Bins contain genes as amino acids instead of nucleotide contigs?" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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54 </xml>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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55 <xml name="tree_params">
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56 <param argument="--reduced_tree" type="boolean" truevalue="--reduced_tree" falsevalue="" checked="false" label="Use reduced tree for determining lineage of each bin?" help="This option requires less than 16GB of memory"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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57 <expand macro="ali" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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58 <expand macro="nt" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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59 <expand macro="genes" />
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60 </xml>
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61 <xml name="tree_extra_output_options">
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62 <option value="hmmer_tree_ali">Phylogenetic HMMER alignment file for each bin</option>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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63 <option value="concatenate_pplacer_json">Concatenated pplacer JSON</option>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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64 <option value="genes_fna">Nucleotide gene sequences for each bin (if generate nucleotide gene sequences)</option>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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65 <option value="genes_faa">Protein gene sequences for each bin</option>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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66 <option value="genes_gff">Gene feature files for each bin (if bins do not contain genes as amino acids instead of nucleotide contigs)</option>
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67 </xml>
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68 <xml name="analyze_params">
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69 <expand macro="ali" />
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70 <expand macro="nt" />
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71 <expand macro="genes" />
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72 </xml>
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73 <xml name="analyze_extra_output_options">
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74 <option value="hmmer_analyze_ali">Marker HMMER alignment file for each bin</option>
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75 </xml>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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76 <xml name="hmm_marker_stats_inputs">
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77 <param name="phylo_hmm_info" type="data" format="zip" label="Phylogenetic HMM model info for each bin" help="Output of the CheckM tree tool"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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78 <param name="bin_stats_tree" type="data" format="tabular" label="Phylogenetic bin stats" help="Output of the CheckM tree tool" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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79 <param name="hmmer_tree" type="data_collection" collection_type="list" format="txt" label="Phylogenetic HMM hits to each bin" help="Output of the CheckM tree tool" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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80 </xml>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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81 <token name="@HMM_MARKER_STATS_INPUTS@"><![CDATA[
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82 #import re
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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83 mkdir -p 'inputs/storage/' &&
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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84 ln -s '$phylo_hmm_info' 'inputs/storage/phylo_hmm_info.pkl.gz' &&
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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85 ln -s '$bin_stats_tree' 'inputs/storage/bin_stats.tree.tsv' &&
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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86 #for $i in $hmmer_tree
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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87 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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88 mkdir -p 'inputs/bins/${identifier}' &&
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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89 ln -s '$i' 'inputs/bins/${identifier}/hmmer.tree.txt' &&
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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90 #end for
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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91 ]]></token>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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92 <xml name="lineage_set_params">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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93 <param argument="--unique" type="integer" min="0" value="10" label="Minimum number of unique phylogenetic markers required to use lineage-specific marker set" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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94 <param argument="--multi" type="integer" min="0" value="10" label="Maximum number of multi-copy phylogenetic markers before defaulting to domain-level marker set " />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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95 <param argument="--force_domain" type="boolean" truevalue="--force_domain" falsevalue="" checked="false" label="Use domain-level sets for all bins?" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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96 <param argument="--no_refinement" type="boolean" truevalue="--no_refinement" falsevalue="" checked="false" label="Do not perform lineage-specific marker set refinement?" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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97 </xml>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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98 <xml name="marker_file">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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99 <param name="marker_file" type="data" format="tabular" label="Marker for assessing bins" help="Each marker to exclude should be listed on a separate line of the file. Output of the CheckM lineage_set or taxon_set tools"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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100 </xml>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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101 <xml name="marker_output">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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102 <data name="marker" format="tabular" label="${tool.name} on ${on_string}: Marker genes"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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103 </xml>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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104 <xml name="qa_params">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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105 <param argument="--individual_markers" type="boolean" truevalue="--individual_markers" falsevalue="" checked="false" label="Treat marker as independent?" help="It will ignore co-located set structure"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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106 <param argument="--skip_adj_correction" type="boolean" truevalue="--skip_adj_correction" falsevalue="" checked="false" label="Do not exclude adjacent marker genes when estimating contamination?"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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107 <param argument="--skip_pseudogene_correction" type="boolean" truevalue="--skip_pseudogene_correction" falsevalue="" checked="false" label="Skip identification and filtering of pseudogenes?"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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108 <param argument="--aai_strain" type="float" min="0" max="1" value="0.9" label="AAI threshold used to identify strain heterogeneity"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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109 <param argument="--ignore_thresholds" type="boolean" truevalue="--ignore_thresholds" falsevalue="" checked="false" label="Ignore model-specific score thresholds?"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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110 <param argument="--e_value" type="float" min="0" max="1" value="1e-10" label="E-value cut off"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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111 <param argument="--length" type="float" min="0" max="1" value="0.7" label="Percent overlap between target and query"/>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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112 </xml>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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113 <xml name="qa_extra_output_options">
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114 <!--<option value="alignment_file">Alignment of multi-copy genes and their AAI identity</option>-->
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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115 <option value="marker_gene_stats">Marker gene stats</option>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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116 </xml>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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117 <xml name="qa_extra_outputs">
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118 <!--<data name="alignment_file" format="tabular" label="${tool.name} on ${on_string}: Alignment of multi-copy genes and their AAI identity" >
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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119 <filter>'alignment_file' in extra_outputs</filter>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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120 </data>-->
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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121 <data name="marker_gene_stats" format="tabular" from_work_dir="output/storage/marker_gene_stats.tsv" label="${tool.name} on ${on_string}: Marker gene statistics">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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122 <filter>'marker_gene_stats' in extra_outputs</filter>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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123 </data>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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124 </xml>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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125 <xml name="rank_taxon">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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126 <conditional name="rank_taxon">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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127 <param argument="--rank" type="select" label="Taxonomic rank">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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128 <option value="life">Life</option>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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129 <option value="domain">Domain</option>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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130 <option value="phylum">Phylum</option>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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131 <option value="order">Order</option>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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132 <option value="family">Family</option>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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133 <option value="genus">Genus</option>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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134 <option value="species">Species</option>
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135 </param>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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136 <when value="life">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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137 <param name="taxon" type="select" label="Taxon of interest" >
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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138 <options from_data_table="life_taxons">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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139 <validator message="No taxon database is available" type="no_options" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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140 </options>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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141 </param>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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142 </when>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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143 <when value="domain">
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144 <param name="taxon" type="select" label="Taxon of interest" >
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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145 <options from_data_table="domain_taxons">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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146 <validator message="No taxon database is available" type="no_options" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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147 </options>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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148 </param>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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149 </when>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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150 <when value="phylum">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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151 <param name="taxon" type="select" label="Taxon of interest" >
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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152 <options from_data_table="phylum_taxons">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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153 <validator message="No taxon database is available" type="no_options" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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154 </options>
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155 </param>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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156 </when>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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diff changeset
157 <when value="order">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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158 <param name="taxon" type="select" label="Taxon of interest" >
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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159 <options from_data_table="order_taxons">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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160 <validator message="No taxon database is available" type="no_options" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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161 </options>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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162 </param>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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163 </when>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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164 <when value="family">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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165 <param name="taxon" type="select" label="Taxon of interest" >
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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166 <options from_data_table="family_taxons">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
parents:
diff changeset
167 <validator message="No taxon database is available" type="no_options" />
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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168 </options>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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169 </param>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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170 </when>
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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171 <when value="genus">
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172 <param name="taxon" type="select" label="Taxon of interest" >
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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173 <options from_data_table="genus_taxons">
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174 <validator message="No taxon database is available" type="no_options" />
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175 </options>
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176 </param>
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177 </when>
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178 <when value="species">
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179 <param name="taxon" type="select" label="Taxon of interest" >
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180 <options from_data_table="species_taxons">
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181 <validator message="No taxon database is available" type="no_options" />
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182 </options>
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183 </param>
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184 </when>
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185 </conditional>
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186 </xml>
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187 <xml name="version">
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188 <version_command>checkm</version_command>
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189 </xml>
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190 <token name="@HELP_HEADER@"><![CDATA[
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191 What it does
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192 ============
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193
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194 CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage. Assessment of genome quality can also be examined using plots depicting key genomic characteristics (e.g., GC, coding density) which highlight sequences outside the expected distributions of a typical genome. CheckM also provides tools for identifying genome bins that are likely candidates for merging based on marker set compatibility, similarity in genomic characteristics, and proximity within a reference genome tree.
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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195 ]]></token>
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196 <token name="@HELP_BINS@"><![CDATA[
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197 - Bins
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198 ]]></token>
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199 <token name="@HELP_TREE_DEFAULT_OUTPUTS@"><![CDATA[
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200 - Phylogenetic HMM model info for each bin
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201 - Phylogenetic bin stats
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202 - Phylogenetic HMM hits to each bin
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203 - Concatenated masked sequences
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204 - Concatenated tree
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205 ]]></token>
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206 <token name="@HELP_TREE_EXTRA_OUTPUTS@"><![CDATA[
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207
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208
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209 <collection name="hmmer_tree_ali" type="list" label="${tool.name} on ${on_string}: Phylogenetic HMMER alignment file for each bin">
b39999cdbf21 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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210 <filter>ali and 'hmmer_tree_ali' in extra_outputs</filter>
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211 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
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212 </collection>
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213 <data name="concatenated_pplacer_json" format="json" from_work_dir="output/storage/tree/concatenated.pplacer.json" label="${tool.name} on ${on_string}: Concatenated pplacer JSON">
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214 <filter>'concatenate_pplacer_json' in extra_outputs</filter>
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215 </data>
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216 <collection name="genes_fna" type="list" label="${tool.name} on ${on_string}: Protein gene sequences for each bin">
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217 <filter>not genes and nt and 'genes_fna' in extra_outputs</filter>
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218 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.fna" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/>
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219 </collection>
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220 <collection name="genes_faa" type="list" label="${tool.name} on ${on_string}: Nucleotide gene sequences for each bin">
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221 <filter>'genes_faa' in extra_outputs</filter>
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222 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.faa" format="fasta" directory="output/bins/" recurse="true" match_relative_path="true"/>
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223 </collection>
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224 <collection name="genes_gff" type="list" label="${tool.name} on ${on_string}: Gene feature files for each bin">
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225 <filter>not genes and 'genes_gff' in extra_outputs</filter>
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226 <discover_datasets pattern="(?P&lt;designation&gt;.*)/genes\.gff" format="gff" directory="output/bins/" recurse="true" match_relative_path="true"/>
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227 </collection>
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228 ]]></token>
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229 <xml name="citations">
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230 <citations>
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231 <citation type="doi">10.1101/gr.186072.114</citation>
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232 </citations>
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233 </xml>
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234 </macros>