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planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
author ufz
date Fri, 25 Jul 2025 10:54:22 +0000
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65d952c59d8b planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/eukcc commit ea26eabce05391af21e0919ac5309d23396960e3
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1 <tool id="eukcc_single" name="EukCC" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0" license="MIT">
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2 <description>estimate completeness and contamination of a novel eukaryotic MAG</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">eukcc</xref>
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8 </xrefs>
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9 <expand macro="requirements"/>
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10 <expand macro="version_command"/>
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11 <command detect_errors="exit_code"><![CDATA[
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12 #import re
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13 #set $identifier= re.sub(r'[^\w\-.]', '_', $fasta.element_identifier)
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14 ln -s '$fasta' '$identifier' &&
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15 mkdir output/ &&
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16 eukcc single
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17 --out output/
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18 --db '$db.fields.path'
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19 --threads "\${GALAXY_SLOTS:-1}"
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20 ## --threads_epa THREADS_EPA
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21 ## Number of threads to use for epa-ng, recommended: 1 (Default: 1)
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22 '$identifier'
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23 $sequence_type
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24 #if str($advanced.taxids) != ""
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25 --taxids $advanced.taxids
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26 #end if
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27 #if $advanced.genomes
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28 --genomes
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29 #for $genome in $advanced.genomes
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30 '$genome'
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31 #end for
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32 #end if
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33 --set_size $advanced.set_size
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34 #if $advanced.use_placement
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35 --use_placement '$advanced.use_placement'
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36 #end if
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37 --set_number_species $advanced.set_number_species
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38 --marker_prevalence $advanced.marker_prevalence
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39 --max_set_size $advanced.max_set_size
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40 $advanced.marker_gene_selection
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41 $advanced.use_ncbi_tree
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42 ## --gmes Use GeneMark-ES instead of metaeuk (much slower) (default: False)
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43 ## --ignore_tree Advanced option, mainly for debugging. Can ignore the tree if genomes are knwon via taxids for example
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44 $advanced.simple
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45 --clade $advanced.clade
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46 ## --rerun, -r Rerun and remove any previously computed data in the target folder
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47 $advanced.no_dynamic_root
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48 $advanced.extra
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49 ## remove header and path to job working dir from output
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50 && tail -n +2 output/eukcc.csv | sed "s|\$(pwd)/\?||" > '$eukcc'
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51 #if $advanced.extra
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52 && gzip -d -c output/scmg_marker_table.csv.gz | tail -n +2 > '$scmg_marker_table'
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53 #end if
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54 ]]></command>
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55 <inputs>
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56 <param name="fasta" type="data" format="fasta" label="A single bin" help="Estimate quality of this bin"/>
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57 <param argument="--db" type="select" label="Reference data">
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58 <options from_data_table="eukcc">
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59 <validator type="no_options" message="Built-in reference is not available. Contact the Galaxy Admin" />
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60 </options>
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61 </param>
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62 <param name="sequence_type" type="select" label="Sequence type">
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63 <option value="">Auto</option>
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64 <option value="--DNA">DNA</option>
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65 <option value="--AA">AA</option>
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66 </param>
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67 <section name="advanced" title="Advanced options" expanded="false">
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68 <param argument="--taxids" type="text" label="Taxids to use as set starting point">
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69 <validator type="regex" message="Must be a space separated list of tax IDs">^[0-9 ]*$</validator>
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70 </param>
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71 <param argument="--genomes" type="data" format="fasta" optional="true" multiple="true" label="Genome files to base a SCMG set upon"/>
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72 <param argument="--set_size" type="integer" min="0" value="20" label="Minimal number of marker genes to use" help="" />
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73 <param argument="--use_placement" type="data" format="csv" optional="true" label="Previous result" help="to use exact same marker gene set" />
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74 <param argument="--set_number_species" type="integer" min="1" value="3" label="Minimal number of species to define a set" help="" />
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75 <param argument="--marker_prevalence" type="float" min="0" max="100" value="95" label="Percentage of species in which markers should be found" help="" />
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76 <param argument="--max_set_size" type="integer" min="0" value="500" label="Maximal number of marker genes used" help="set to 0 to include all possible marker genes" />
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77 <param name="marker_gene_selection" type="select" label="Marker gene selection method" help="">
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78 <option value="--select_best_guess">Use best guess to select marker gene set</option>
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79 <option value="--select_species">Use species count to select best marker gene set</option>
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80 </param>
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81 <param argument="--use_ncbi_tree" type="boolean" truevalue="--use_ncbi_tree" falsevalue="" checked="false" label="Use NCBI tree" help="Instead of using the EukCC phylogenetic tree, rely on NCBI taxids" />
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82 <param argument="--simple" type="boolean" truevalue="--simple" falsevalue="" checked="false" label="Use global DB instead of clade specific DBs" help="faster, not suitable for protozoa" />
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83 <param argument="--clade" type="select" label="Define clade as base">
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84 <option value="base">Root</option>
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85 <option value="fungi">Fungi</option>
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86 <option value="protozoa">Protozoa</option>
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87 <option value="plants">Plants</option>
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88 </param>
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89 <param argument="--no_dynamic_root" type="boolean" truevalue="" falsevalue="--no_dynamic_root" checked="false" label="re-root tree dynamically" help="Disable for best set detection" />
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90 <param argument="--extra" type="boolean" truevalue="--extra" falsevalue="" checked="false" label="Produce extra outputs" />
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91 </section>
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92 </inputs>
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93 <outputs>
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94 <data name="eukcc" format="tabular">
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95 <actions>
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96 <action type="metadata" name="column_names" default="fasta,completeness,contamination,ncbi_lng"/>
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97 </actions>
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98 </data>
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99 <data name="scmg_marker_table" format="tabular" label="${tool.name} on ${on_string}: SCMG marker table">
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100 <filter>advanced['extra']</filter>
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101 <actions>
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102 <action type="metadata" name="column_names" default="target,query,bitscore,evalue,expected_GA"/>
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103 </actions>
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104 </data>
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105 </outputs>
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106 <tests>
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107 <!-- reference data to large for test in CI. Download locally with test-data.sh to run tests.
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108 <test expect_num_outputs="1">
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109 <param name="fasta" value="10000_lines_GCA_903798045.1_TARA_EukCC_1_genomic.fna"/>
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110 <param name="db" value="1.2"/>
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111 <output name="eukcc">
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112 <assert_contents>
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113 <has_text text="GCA_903798045.1"/>
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114 <has_text text="41874"/> <!\-\- 41874 = Bathycoccus \-\->
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115 <has_n_lines n="1"/>
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116 <has_n_columns n="4"/>
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117 </assert_contents>
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118 </output>
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119 </test>
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120 <test expect_num_outputs="2">
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121 <param name="fasta" value="10000_lines_GCA_903798045.1_TARA_EukCC_1_genomic.fna"/>
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122 <param name="db" value="1.2"/>
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123 <section name="advanced">
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124 <param name="extra" value="true"/>
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125 </section>
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126 <output name="eukcc">
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127 <assert_contents>
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128 <has_text text="GCA_903798045.1"/>
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129 <has_n_lines n="1"/>
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130 <has_n_columns n="4"/>
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131 </assert_contents>
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132 </output>
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133 <output name="scmg_marker_table">
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134 <assert_contents>
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135 <has_n_lines n="314"/>
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136 <has_n_columns n="5"/>
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137 </assert_contents>
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138 </output>
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139 </test> -->
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140 </tests>
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141 <help><![CDATA[
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142
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143 .. class:: infomark
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144
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145 **What it does**
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146
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147 It consumes bins in FASTA format and outputs a table with estimated completeness, contamination and taxonomy lineage (given as dash separated list of TaxIDs).
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148
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149 You should not use EukCC on already published genomes, if they have used during training of the marker gene sets.
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150 If you want to make sure, you can see all used accessions in the database file db_base/backbone/base_taxinfo.csv.
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151
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152 ]]></help>
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153 <citations>
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154 <citation type="doi">10.1186/s13059-020-02155-4</citation>
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155 </citations>
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156 </tool>