Mercurial > repos > iuc > checkm_tree_qa

annotate macros.xml @ 0:dd51f61c2309 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 20:30:47 +0000
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children b9a38ce53252
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dd51f61c2309 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"?>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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2 <macros>
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3 <token name="@TOOL_VERSION@">1.2.0</token>
dd51f61c2309 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>
dd51f61c2309 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>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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6 <xml name="biotools">
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7 <xrefs>
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8 <xref type="bio.tools">checkm</xref>
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9 </xrefs>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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10 </xml>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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11 <xml name="requirements">
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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12 <requirements>
dd51f61c2309 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>
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14 <yield/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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15 </requirements>
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16 </xml>
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17 <xml name="bin_inputs">
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18 <conditional name="bins">
dd51f61c2309 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">
dd51f61c2309 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>
dd51f61c2309 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>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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22 </param>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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23 <when value="collection">
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24 <param name="bins_coll" type="data_collection" collection_type="list" format="fasta" label="Bins"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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25 </when>
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26 <when value="individual">
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27 <param name="bins_ind" type="data" format="fasta" multiple="true" label="Bins"/>
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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28 </when>
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29 </conditional>
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30 </xml>
dd51f61c2309 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[
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32 #import re
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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33 mkdir 'bins' &&
dd51f61c2309 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'
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35 #for $b in $bins.bins_coll
dd51f61c2309 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))
dd51f61c2309 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' &&
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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38 #end for
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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39 #else
dd51f61c2309 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
dd51f61c2309 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))
dd51f61c2309 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' &&
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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43 #end for
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44 #end if
dd51f61c2309 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/checkm commit 2a3b068a98bf0e913dc03e0d5c2182cfd102cf27
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45 ]]></token>
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46 <xml name="ali">
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47 <param argument="--ali" type="boolean" truevalue="--ali" falsevalue="" checked="false" label="Generate HMMER alignment file for each bin?" />
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48 </xml>
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49 <xml name="nt">
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50 <param argument="--nt" type="boolean" truevalue="--nt" falsevalue="" checked="false" label="Generate nucleotide gene sequences for each bin?" />
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51 </xml>
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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?" />
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54 </xml>
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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"/>
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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>
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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>
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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>
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65 <option value="genes_faa">Protein gene sequences for each bin</option>
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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>
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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"/>
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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" />
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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" />
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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
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83 mkdir -p 'inputs/storage/' &&
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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' &&
dd51f61c2309 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
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87 #set $identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier))
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88 mkdir -p 'inputs/bins/${identifier}' &&
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89 ln -s '$i' 'inputs/bins/${identifier}/hmmer.tree.txt' &&
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90 #end for
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91 ]]></token>
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92 <xml name="lineage_set_params">
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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" />
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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 " />
dd51f61c2309 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?" />
dd51f61c2309 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?" />
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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"/>
dd51f61c2309 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?"/>
dd51f61c2309 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?"/>
dd51f61c2309 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"/>
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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"/>
dd51f61c2309 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">
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122 <filter>'marker_gene_stats' in extra_outputs</filter>
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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">
dd51f61c2309 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>
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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" >
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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 ${on_string}: Concatenated pplacer JSON">
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214 <filter>'concatenate_pplacer_json' in extra_outputs</filter>
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215 </data>
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216 <collection name="genes_fna" type="list" label="${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>