Mercurial > repos > iuc > gtdbtk_classify_wf

annotate gtdbtk_classify_wf.xml @ 6:a09c8c901603 draft

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author iuc
date Fri, 13 Sep 2024 11:15:36 +0000
parents a68b985913ab
children b907a3c0434f
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1 <tool id="gtdbtk_classify_wf" name="GTDB-Tk Classify genomes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>by placement in GTDB reference tree</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <xrefs>
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7 <xref type="bio.tools">GTDB-Tk</xref>
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8 </xrefs>
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9 <expand macro="requirements"/>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #import re
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13 mkdir input_dir &&
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14 mkdir output_dir &&
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15 #for $i in $input:
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16 ## gtdbtk uses the file extension to determine the input format.
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17 #set ext = "." + $i.ext
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18 #set input_identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) + $ext
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19 ln -s '${i}' input_dir/'${input_identifier}' &&
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20 #end for
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21 export GTDBTK_DATA_PATH=$gtdbtk_db.fields.path &&
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22 gtdbtk classify_wf
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23 --genome_dir input_dir
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24 --extension '$ext'
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25 --out_dir output_dir
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26 --cpus \${GALAXY_SLOTS:-4}
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27 --min_perc_aa $advanced.min_perc_aa
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28 $advanced.force
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29 --min_af $advanced.min_af
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30
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31 ## Required unless mash_db is available:
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32 --skip_ani_screen
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33
0
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34 #if str($advanced.output_process_log) == 'yes':
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35 && cat output_dir/gtdbtk.warnings.log output_dir/gtdbtk.log > '$process_log'
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36 #end if
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37 ]]></command>
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38 <inputs>
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39 <param name="input" type="data" format="fasta,fasta.gz" multiple="true" label="Fasta (Genome) files"/>
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40 <param name="gtdbtk_db" type="select" label="GTDB-Tk database" help="This version of GTDB-Tk required GTDB version R207_v2. Please contact your service administrator if this version is not available to select.">
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41 <options from_data_table="gtdbtk_database_versioned">
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42 <filter type="regexp" column="3" value="^v2(07|14)$"/>
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43 <validator type="no_options" message="No locally cached GTDB-Tk database is available"/>
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44 </options>
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45 </param>
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46 <section name="advanced" title="Advanced options">
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47 <param argument="--min_perc_aa" type="integer" min="0" max="100" value="10" label="Exclude genomes that do not have at least this percentage of AA in the MSA" help="Inclusive bound"/>
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48 <param argument="--force" type="boolean" truevalue="--force" falsevalue="" checked="false" label="Continue processing if an error occurs on a single genome?"/>
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49 <param argument="--min_af" type="float" min="0" max="1" value="0.65" label="Minimum alignment fraction to consider closest genome"/>
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50 <param name="output_process_log" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output process log file?"/>
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51 </section>
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52 </inputs>
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53 <outputs>
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54 <data name="process_log" format="txt" label="${tool.name} on ${on_string} (process log)">
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55 <filter>advanced['output_process_log']</filter>
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56 </data>
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57 <collection name="output_align" type="list" format="fasta.gz" label="${tool.name} on ${on_string} (align)">
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58 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta.gz" ext="fasta.gz" directory="output_dir/align"/>
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59 </collection>
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60 <collection name="output_identfy" type="list" format="tsv" label="${tool.name} on ${on_string} (identify)">
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61 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" ext="tsv" directory="output_dir/identify"/>
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62 </collection>
2
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63 <collection name="output_classify" type="list" format="newick" label="${tool.name} on ${on_string} (classify)">
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64 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tree" ext="newick" directory="output_dir/classify"/>
0
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65 </collection>
2
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66 <collection name="output_summary" type="list" format="tsv" label="${tool.name} on ${on_string} (summary)">
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67 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tsv" ext="tsv" directory="output_dir"/>
0
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68 </collection>
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69 </outputs>
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70 <tests>
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71 <!-- The commented test here is valid if we could store the GTDB-Tk database -->
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72 <!--
2
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73 <test expect_num_outputs="4">
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74 <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/>
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75 <param name="gtdbtk_db" value="gtdbtk214"/>
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76 <output_collection name="output_summary" type="list" count="1">
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77 <element name="gtdbtk.ar53.summary" ftype="tsv">
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78 <assert_contents>
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79 <has_text text="user_genome"/>
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80 </assert_contents>
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81 </element>
2
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82 </output_collection>
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83 <output_collection name="output_identfy" type="list" count="4">
4
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84 <element name="gtdbtk.ar53.markers_summary" ftype="tsv">
0
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85 <assert_contents>
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86 <has_text text="number_unique_genes"/>
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87 </assert_contents>
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88 </element>
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89 <element name="gtdbtk.bac120.markers_summary" ftype="tsv">
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90 <assert_contents>
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91 <has_text text="genome_1_fna_gz"/>
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92 </assert_contents>
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93 </element>
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94 <element name="gtdbtk.failed_genomes" ftype="tsv">
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95 <assert_contents>
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96 <has_size value="0"/>
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97 </assert_contents>
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98 </element>
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99 <element name="gtdbtk.translation_table_summary" ftype="tsv">
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100 <assert_contents>
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101 <has_text text="genome_1_fna_gz"/>
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102 </assert_contents>
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103 </element>
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104 </output_collection>
4
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105 <output_collection name="output_classify" type="list" count="1">
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106 <element name="gtdbtk.ar53.classify" ftype="newick">
0
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107 <assert_contents>
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108 <has_text text="GB_GCA_"/>
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109 </assert_contents>
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110 </element>
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111 </output_collection>
2
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112 <output_collection name="output_align" type="list" count="2">
4
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113 <element name="gtdbtk.ar53.msa" ftype="fasta.gz" decompress="true">
0
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114 <assert_contents>
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115 <has_text text="GB_GCA_000008085"/>
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116 </assert_contents>
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117 </element>
4
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118 <element name="gtdbtk.ar53.user_msa" ftype="fasta.gz" decompress="true">
0
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119 <assert_contents>
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120 <has_text text="genome_1_fna_gz"/>
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121 </assert_contents>
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122 </element>
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123 </output_collection>
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124 </test>
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125 -->
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126 <!-- GTDB-Tk databases are far too large to test currently -->
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127 <test expect_failure="true">
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128 <param name="input" value="genome_1.fna.gz" ftype="fasta.gz"/>
6
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129 <param name="gtdbtk_db" value="gtdbtk214"/>
0
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130 <assert_stderr>
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131 <has_text text="Fatal error: Exit code 1"/>
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132 </assert_stderr>
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133 </test>
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134 </tests>
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135 <help><![CDATA[
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136 **What it does**
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137
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138 GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes
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139 based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or
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140 thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also
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141 be applied to isolate and single-cell genomes.
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142
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143 This tool accepts one or more fasta (genome) files and determines taxonomic classification of genomes by
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144 maximum-likelihood (ML) placement. The classification workflow consists of three steps: identify, align, and
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145 classify.
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146
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147 The identify step calls genes using Prodigal, and uses HMM models and the HMMER package to identify the 120 bacterial
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148 and 122 archaeal marker genes used for phylogenetic inference. Multiple sequence alignments (MSA) are obtained by
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149 aligning marker genes to their respective HMM model.
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150
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151 The align step concatenates the aligned marker genes and filters the concatenated MSA to approximately 5,000
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152 amino acids.
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153
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154 Finally, the classify step uses pplacer to find the maximum-likelihood placement of each genome in the GTDB-Tk
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155 reference tree. GTDB-Tk classifies each genome based on its placement in the reference tree, its relative evolutionary
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156 divergence, and/or average nucleotide identity (ANI) to reference genomes.
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157
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158 Results can be impacted by a lack of marker genes or contamination.
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159 ]]></help>
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160 <expand macro="citations"/>
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161 </tool>
2
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162