annotate gecco.xml @ 10:9156eb4ee20c draft

"Release v0.9.1-alpha1"
author althonos
date Sun, 20 Mar 2022 15:44:07 +0000
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool id="gecco" name="GECCO" version="0.8.10" 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 <requirements>
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5 <requirement type="package" version="0.8.10">gecco</requirement>
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6 </requirements>
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7 <version_command>gecco --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9
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10 #if str($input.ext) == 'genbank':
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11 #set $file_extension = 'gbk'
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12 #else:
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13 #set $file_extension = $input.ext
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14 #end if
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15 ln -s '$input' input_tempfile.$file_extension &&
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16
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17 gecco -vv run
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18 --format $input.ext
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19 --genome input_tempfile.$file_extension
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20 --postproc $postproc
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21 --edge-distance $edge_distance
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22 --force-clusters-tsv
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23 #if $mask
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24 --mask
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25 #end if
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26 #if $cds:
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27 --cds $cds
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28 #end if
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29 #if $threshold:
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30 --threshold $threshold
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31 #end if
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32 #if $antismash_sideload:
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33 --antismash-sideload
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34 #end if
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35
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36 && mv input_tempfile.features.tsv '$features'
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37 && mv input_tempfile.clusters.tsv '$clusters'
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38 #if $antismash_sideload
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39 && mv input_tempfile.sideload.json '$sideload'
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40 #end if
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41
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42 ]]></command>
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43 <inputs>
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44 <param name="input" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank, EMBL or FASTA format"/>
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45 <param argument="--mask" type="boolean" checked="false" label="Enable masking of regions with unknown nucleotides when finding ORFs"/>
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46 <param argument="--cds" type="integer" min="0" value="" optional="true" label="Minimum number of genes required for a cluster"/>
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47 <param argument="--threshold" type="float" min="0" max="1" value="" optional="true" label="Probability threshold for cluster detection"/>
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48 <param argument="--postproc" type="select" label="Post-processing method for gene cluster validation">
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49 <option value="antismash">antiSMASH</option>
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50 <option value="gecco" selected="true">GECCO</option>
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51 </param>
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52 <param argument="--edge-distance" type="integer" min="0" value="10" label="Number of genes from the contig edges to filter out"/>
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53 <param argument="--antismash-sideload" type="boolean" checked="false" label="Generate an antiSMASH v6 sideload JSON file"/>
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54 </inputs>
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55 <outputs>
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56 <collection name="records" type="list" label="${tool.name} detected Biosynthetic Gene Clusters on ${on_string} (GenBank)">
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57 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gbk" ext="genbank" visible="false" />
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58 </collection>
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59 <data name="features" format="tabular" label="${tool.name} summary of detected features on ${on_string} (TSV)"/>
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60 <data name="clusters" format="tabular" label="${tool.name} summary of detected BGCs on ${on_string} (TSV)"/>
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61 <data name="sideload" format="json" label="antiSMASH v6 sideload file with ${tool.name} detected BGCs on ${on_string} (JSON)">
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62 <filter>antismash_sideload</filter>
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63 </data>
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="input" value="BGC0001866.fna"/>
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68 <output name="features" file="features.tsv"/>
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69 <output name="clusters" file="clusters.tsv"/>
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70 </test>
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71 <test>
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72 <param name="input" value="BGC0001866.fna"/>
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73 <param name="edge_distance" value="0"/>
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74 <output name="features" file="features.tsv"/>
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75 <output name="clusters" file="clusters.tsv"/>
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76 <output_collection name="records" type="list">
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77 <element name="BGC0001866.1_cluster_1" file="BGC0001866.1_cluster_1.gbk" ftype="genbank" compare="diff" lines_diff="4"/>
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78 </output_collection>
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79 </test>
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80 <test>
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81 <param name="input" value="BGC0001866.fna"/>
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82 <param name="antismash_sideload" value="True"/>
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83 <param name="edge_distance" value="0"/>
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84 <output name="features" file="features.tsv"/>
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85 <output name="clusters" file="clusters.tsv"/>
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86 <output name="sideload" file="sideload.json"/>
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87 <output_collection name="records" type="list">
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88 <element name="BGC0001866.1_cluster_1" file="BGC0001866.1_cluster_1.gbk" ftype="genbank" compare="diff" lines_diff="4"/>
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89 </output_collection>
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90 </test>
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91 </tests>
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92 <help><![CDATA[
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93
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94 Overview
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95 --------
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96
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97 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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98 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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99
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100 Input
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101 -----
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102
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103 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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104
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105 Output
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106 ------
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107
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108 GECCO will create the following files once done (using the same prefix as the input file):
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109
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110 - ``features.tsv``: The features file, containing the identified proteins and domains in the input sequences.
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111 - ``clusters.tsv``: If any were found, a clusters file, containing the coordinates of the predicted clusters, along their putative biosynthetic type.
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112 - ``{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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113
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114 Contact
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115 -------
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116
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117 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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118 `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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119 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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120
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121 ]]></help>
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122 <citations>
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123 <citation type="doi">10.1101/2021.05.03.442509</citation>
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124 </citations>
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125 </tool>