annotate gecco.xml @ 20:64b724dd8d04 draft

Regenerate Galaxy test files with Pyrodigal `v2.1.0`
author althonos
date Mon, 27 Mar 2023 13:32:49 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool id="gecco" name="GECCO" version="0.9.6" python_template_version="3.5">
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3 <description>is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs).</description>
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4 <creator>
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5 <organization name="Zeller Team" url="https://www.embl.org/groups/zeller/"/>
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6 </creator>
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7 <edam_topics>
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8 <edam_topic>topic_0080</edam_topic>
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9 </edam_topics>
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10 <edam_operations>
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11 <edam_operation>operation_0415</edam_operation>
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12 </edam_operations>
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13 <requirements>
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14 <requirement type="package" version="0.9.6">gecco</requirement>
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15 </requirements>
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16 <version_command>gecco --version</version_command>
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17 <command detect_errors="aggressive"><![CDATA[
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18
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19 #if str($input.ext) == 'genbank':
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20 #set $file_extension = 'gbk'
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21 #else:
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22 #set $file_extension = $input.ext
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23 #end if
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24 ln -s '$input' input_tempfile.$file_extension &&
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25
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26 gecco -vv run
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27 --format $input.ext
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28 --genome input_tempfile.$file_extension
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29 --postproc $postproc
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30 --force-tsv
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31 --jobs "\${GALAXY_SLOTS:-4}"
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32 #if $edge_distance
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33 --edge-distance $edge_distance
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34 #end if
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35 #if $mask
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36 --mask
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37 #end if
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38 #if $cds:
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39 --cds $cds
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40 #end if
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41 #if $threshold:
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42 --threshold $threshold
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43 #end if
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44 #if $antismash_sideload:
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45 --antismash-sideload
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46 #end if
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47 #unless $pad:
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48 --no-pad
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49 #end unless
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50
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51 && mv input_tempfile.genes.tsv '$genes'
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52 && mv input_tempfile.features.tsv '$features'
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53 && mv input_tempfile.clusters.tsv '$clusters'
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54 #if $antismash_sideload
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55 && mv input_tempfile.sideload.json '$sideload'
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56 #end if
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57
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58 ]]></command>
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59 <inputs>
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60 <param name="input" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank, EMBL or FASTA format"/>
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61 <param argument="--mask" type="boolean" checked="false" label="Enable masking of regions with unknown nucleotides when finding ORFs"/>
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62 <param argument="--pad" type="boolean" checked="true" label="Enable padding of gene sequences smaller than the CRF window length"/>
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63 <param argument="--cds" type="integer" min="0" value="" optional="true" label="Minimum number of genes required for a cluster"/>
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64 <param argument="--threshold" type="float" min="0" max="1" value="" optional="true" label="Probability threshold for cluster detection"/>
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65 <param argument="--postproc" type="select" label="Post-processing method for gene cluster validation">
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66 <option value="antismash">antiSMASH</option>
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67 <option value="gecco" selected="true">GECCO</option>
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68 </param>
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69 <param argument="--edge-distance" type="integer" min="0" optional="true" value="" label="Number of genes from the contig edges to filter out"/>
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70 <param argument="--antismash-sideload" type="boolean" checked="false" label="Generate an antiSMASH v6 sideload JSON file"/>
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71 </inputs>
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72 <outputs>
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73 <collection name="records" type="list" label="${tool.name} detected Biosynthetic Gene Clusters on ${on_string} (GenBank)">
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74 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gbk" ext="genbank" visible="false" />
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75 </collection>
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76 <data name="genes" format="tabular" label="${tool.name} summary of detected genes on ${on_string} (TSV)"/>
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77 <data name="features" format="tabular" label="${tool.name} summary of detected features on ${on_string} (TSV)"/>
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78 <data name="clusters" format="tabular" label="${tool.name} summary of detected BGCs on ${on_string} (TSV)"/>
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79 <data name="sideload" format="json" label="antiSMASH v6 sideload file with ${tool.name} detected BGCs on ${on_string} (JSON)">
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80 <filter>antismash_sideload</filter>
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81 </data>
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82 </outputs>
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83 <tests>
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84 <test>
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85 <param name="input" value="BGC0001866.fna"/>
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86 <output name="features" file="features.tsv"/>
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87 <output name="genes" file="genes.tsv"/>
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88 <output name="clusters" file="clusters.tsv"/>
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89 <param name="edge_distance" value="10"/>
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90 </test>
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91 <test>
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92 <param name="input" value="BGC0001866.fna"/>
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93 <output name="features" file="features.tsv"/>
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94 <output name="genes" file="genes.tsv"/>
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95 <output name="clusters" file="clusters.tsv"/>
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96 <output_collection name="records" type="list">
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97 <element name="BGC0001866.1_cluster_1" file="BGC0001866.1_cluster_1.gbk" ftype="genbank" compare="diff" lines_diff="4"/>
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98 </output_collection>
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99 </test>
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100 <test>
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101 <param name="input" value="BGC0001866.fna"/>
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102 <param name="antismash_sideload" value="True"/>
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103 <output name="features" file="features.tsv"/>
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104 <output name="genes" file="genes.tsv"/>
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105 <output name="clusters" file="clusters.tsv"/>
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106 <output name="sideload" file="sideload.json"/>
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107 <output_collection name="records" type="list">
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108 <element name="BGC0001866.1_cluster_1" file="BGC0001866.1_cluster_1.gbk" ftype="genbank" compare="diff" lines_diff="4"/>
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109 </output_collection>
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110 </test>
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111 </tests>
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112 <help><![CDATA[
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113
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114 Overview
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115 --------
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116
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117 GECCO (Gene Cluster prediction with Conditional Random Fields) is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs).
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118 It is developed in the Zeller group and is part of the suite of computational microbiome analysis tools hosted at EMBL.
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119
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120 Input
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121 -----
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122
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123 GECCO works with DNA sequences, and loads them using Biopython, allowing it to support a large variety of formats, including the common FASTA and GenBank files.
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124
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125 Output
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126 ------
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127
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128 GECCO will create the following files once done (using the same prefix as the input file):
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129
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130 - ``features.tsv``: The genes file, containing the genes identified in the input sequences.
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131 - ``features.tsv``: The features file, containing the protein domains identified in the input sequences.
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132 - ``clusters.tsv``: A clusters file, containing the coordinates of the predicted clusters, along their putative biosynthetic type.
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133 - ``{sequence}_cluster_{N}.gbk``: If any BGCs were found, a GenBank file per cluster, containing the cluster sequence annotated with its member proteins and domains.
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134
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135 Contact
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136 -------
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137
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138 If you have any question about GECCO, if you run into any issue, or if you would like to make a feature request, please create an issue in the
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139 `GitHub repository <https://github.com/zellerlab/gecco>`_. You can also directly contact `Martin Larralde via email <mailto:martin.larralde@embl.de>`_.
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140 If you want to contribute to GECCO, please have a look at the contribution guide first, and feel free to open a pull request on the GitHub repository.
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141
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142 ]]></help>
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143 <citations>
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144 <citation type="doi">10.1101/2021.05.03.442509</citation>
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145 </citations>
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146 </tool>