Mercurial > repos > iuc > checkm_analyze

annotate macros.xml @ 2:bcb8dc01f296 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 3ae2bd72f789518e95ef65b97e0e5ac90165e113
author iuc
date Mon, 02 Sep 2024 13:50:29 +0000
parents 5ee29434330f
children
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7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
iuc
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1 <?xml version="1.0"?>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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2 <macros>
2
bcb8dc01f296 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 3ae2bd72f789518e95ef65b97e0e5ac90165e113
iuc
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3 <token name="@TOOL_VERSION@">1.2.3</token>
0
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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4 <token name="@VERSION_SUFFIX@">0</token>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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5 <token name="@PROFILE@">21.01</token>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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6 <xml name="biotools">
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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7 <xrefs>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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8 <xref type="bio.tools">checkm</xref>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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9 </xrefs>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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10 </xml>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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11 <xml name="requirements">
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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12 <requirements>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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13 <requirement type="package" version="@TOOL_VERSION@">checkm-genome</requirement>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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14 <yield/>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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15 </requirements>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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16 </xml>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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17 <xml name="bin_inputs">
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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18 <conditional name="bins">
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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19 <param name="select" type="select" label="Data structure for bins">
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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20 <option value="collection">In collection</option>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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21 <option value="individual">In individual datasets</option>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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22 </param>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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23 <when value="collection">
7ccea589e8b7 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"/>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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25 </when>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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26 <when value="individual">
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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27 <param name="bins_ind" type="data" format="fasta" multiple="true" label="Bins"/>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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28 </when>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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29 </conditional>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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30 </xml>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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31 <token name="@BIN_INPUTS@"><![CDATA[
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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32 #import re
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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33 mkdir 'bins' &&
7ccea589e8b7 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'
7ccea589e8b7 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
7ccea589e8b7 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))
7ccea589e8b7 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' &&
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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38 #end for
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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39 #else
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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40 #for $b in $bins.bins_ind
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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41 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($b.element_identifier))
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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42 ln -s '$b.file_name' 'bins/${identifier}.fasta' &&
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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43 #end for
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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44 #end if
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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45 ]]></token>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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46 <xml name="ali">
7ccea589e8b7 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?" />
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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48 </xml>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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49 <xml name="nt">
7ccea589e8b7 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?" />
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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51 </xml>
7ccea589e8b7 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?" />
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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54 </xml>
7ccea589e8b7 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">
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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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"/>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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57 <expand macro="ali" />
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58 <expand macro="nt" />
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59 <expand macro="genes" />
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60 </xml>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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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>
7ccea589e8b7 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>
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64 <option value="genes_fna">Nucleotide gene sequences for each bin (if generate nucleotide gene sequences)</option>
7ccea589e8b7 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>
7ccea589e8b7 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>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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75 </xml>
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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"/>
7ccea589e8b7 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" />
7ccea589e8b7 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" />
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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80 </xml>
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81 <token name="@HMM_MARKER_STATS_INPUTS@"><![CDATA[
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82 #import re
7ccea589e8b7 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/' &&
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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84 ln -s '$phylo_hmm_info' 'inputs/storage/phylo_hmm_info.pkl.gz' &&
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85 ln -s '$bin_stats_tree' 'inputs/storage/bin_stats.tree.tsv' &&
7ccea589e8b7 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
7ccea589e8b7 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/${identifier}' &&
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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89 ln -s '$i' 'inputs/bins/${identifier}/hmmer.tree.txt' &&
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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90 #end for
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91 ]]></token>
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92 <xml name="lineage_set_params">
7ccea589e8b7 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" />
7ccea589e8b7 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 " />
7ccea589e8b7 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?" />
7ccea589e8b7 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?" />
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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97 </xml>
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98 <xml name="marker_file">
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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"/>
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100 </xml>
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101 <xml name="marker_output">
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102 <data name="marker" format="tabular" label="${tool.name} on ${on_string}: Marker genes"/>
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103 </xml>
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104 <xml name="qa_params">
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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"/>
7ccea589e8b7 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?"/>
7ccea589e8b7 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?"/>
7ccea589e8b7 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"/>
7ccea589e8b7 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?"/>
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110 <param argument="--e_value" type="float" min="0" max="1" value="1e-10" label="E-value cut off"/>
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111 <param argument="--length" type="float" min="0" max="1" value="0.7" label="Percent overlap between target and query"/>
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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112 </xml>
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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>-->
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115 <option value="marker_gene_stats">Marker gene stats</option>
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116 </xml>
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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 ${on_string}: Alignment of multi-copy genes and their AAI identity" >
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119 <filter>'alignment_file' in extra_outputs</filter>
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120 </data>-->
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121 <data name="marker_gene_stats" format="tabular" from_work_dir="output/storage/marker_gene_stats.tsv" label="${tool.name} on ${on_string}: Marker gene statistics">
1
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122 <filter>extra_outputs and 'marker_gene_stats' in extra_outputs</filter>
0
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123 </data>
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124 </xml>
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125 <xml name="rank_taxon">
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126 <conditional name="rank_taxon">
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127 <param argument="--rank" type="select" label="Taxonomic rank">
7ccea589e8b7 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>
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129 <option value="domain">Domain</option>
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130 <option value="phylum">Phylum</option>
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131 <option value="order">Order</option>
7ccea589e8b7 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>
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133 <option value="genus">Genus</option>
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134 <option value="species">Species</option>
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135 </param>
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136 <when value="life">
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137 <param name="taxon" type="select" label="Taxon of interest" >
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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138 <options from_data_table="life_taxons">
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139 <validator message="No taxon database is available" type="no_options" />
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140 </options>
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141 </param>
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142 </when>
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143 <when value="domain">
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144 <param name="taxon" type="select" label="Taxon of interest" >
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145 <options from_data_table="domain_taxons">
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146 <validator message="No taxon database is available" type="no_options" />
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147 </options>
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148 </param>
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149 </when>
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150 <when value="phylum">
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151 <param name="taxon" type="select" label="Taxon of interest" >
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152 <options from_data_table="phylum_taxons">
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153 <validator message="No taxon database is available" type="no_options" />
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154 </options>
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155 </param>
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156 </when>
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157 <when value="order">
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158 <param name="taxon" type="select" label="Taxon of interest" >
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159 <options from_data_table="order_taxons">
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160 <validator message="No taxon database is available" type="no_options" />
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161 </options>
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162 </param>
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163 </when>
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164 <when value="family">
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165 <param name="taxon" type="select" label="Taxon of interest" >
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166 <options from_data_table="family_taxons">
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167 <validator message="No taxon database is available" type="no_options" />
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168 </options>
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169 </param>
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170 </when>
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171 <when value="genus">
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172 <param name="taxon" type="select" label="Taxon of interest" >
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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.
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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 ${on_string}: Phylogenetic HMMER alignment file for each bin">
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210 <filter>ali and 'hmmer_tree_ali' in extra_outputs</filter>
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211 <discover_datasets pattern="(?P&lt;designation&gt;.*)/hmmer\.tree\.ali\.txt" format="txt" directory="output/bins/" recurse="true" match_relative_path="true"/>
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212 </collection>
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213 <data name="concatenated_pplacer_json" format="json" from_work_dir="output/storage/tree/concatenated.pplacer.json" label="${tool.name} on ${on_string}: Concatenated pplacer JSON">
7ccea589e8b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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214 <filter>'concatenate_pplacer_json' in extra_outputs</filter>
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215 </data>
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216 <collection name="genes_fna" type="list" label="${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>