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annotate gecco.xml @ 3:359232b58f6a draft

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"Update Galaxy tool wrapper to follow the IUC best practices"
author althonos
date Sun, 21 Nov 2021 19:47:22 +0000
parents 1625927fc16f
children 88dc16b4f583
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool id="gecco" name="GECCO" version="0.8.5" 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="0.8.5">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 --force-clusters-tsv
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22 #if $cds:
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23 --cds $cds
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24 #end if
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25 #if $threshold:
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26 --threshold $threshold
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27 #end if
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28 #if $antismash_sideload:
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29 --antismash-sideload
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30 #end if
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31
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32 && mv input_tempfile.features.tsv '$features'
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33 && mv input_tempfile.clusters.tsv '$clusters'
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34 #if $antismash_sideload
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35 && mv input_tempfile.sideload.json '$sideload'
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36 #end if
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37
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38 ]]></command>
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39 <inputs>
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40 <param name="input" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank, EMBL or FASTA format"/>
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41 <param argument="--cds" type="integer" min="0" value="" optional="true" label="Minimum number of genes required for a cluster"/>
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42 <param argument="--threshold" type="float" min="0" max="1" value="" optional="true" label="Probability threshold for cluster detection"/>
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43 <param argument="--postproc" type="select" label="Post-processing method for gene cluster validation">
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44 <option value="antismash">antiSMASH</option>
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45 <option value="gecco" selected="true">GECCO</option>
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46 </param>
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47 <param argument="--antismash-sideload" type="boolean" checked="false" label="Generate an antiSMASH v6 sideload JSON file"/>
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48 </inputs>
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49 <outputs>
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50 <collection name="records" type="list" label="${tool.name} detected Biosynthetic Gene Clusters on ${on_string} (GenBank)">
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51 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gbk" ext="genbank" visible="false" />
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52 </collection>
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53 <data name="features" format="tabular" label="${tool.name} summary of detected features on ${on_string} (TSV)"/>
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54 <data name="clusters" format="tabular" label="${tool.name} summary of detected BGCs on ${on_string} (TSV)"/>
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55 <data name="sideload" format="json" label="antiSMASH v6 sideload file with ${tool.name} detected BGCs on ${on_string} (JSON)">
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56 <filter>antismash_sideload</filter>
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57 </data>
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param name="input" value="BGC0001866.fna"/>
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62 <output name="features" file="features.tsv"/>
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63 <output name="clusters" file="clusters.tsv"/>
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64 <output_collection name="records" type="list">
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65 <element name="BGC0001866.1_cluster_1" file="BGC0001866.1_cluster_1.gbk" ftype="genbank" lines_diff="2"/>
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66 </output_collection>
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67 </test>
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68 <test>
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69 <param name="input" value="BGC0001866.fna"/>
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70 <param name="antismash_sideload" value="True"/>
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71 <output name="features" file="features.tsv"/>
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72 <output name="clusters" file="clusters.tsv"/>
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73 <output name="sideload" file="sideload.json"/>
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74 <output_collection name="records" type="list">
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75 <element name="BGC0001866.1_cluster_1" file="BGC0001866.1_cluster_1.gbk" ftype="genbank" lines_diff="2"/>
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76 </output_collection>
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77 </test>
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78 </tests>
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79 <help><![CDATA[
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80
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81 Overview
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82 --------
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83
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84 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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85 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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86
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87 Input
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88 -----
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89
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90 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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91
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92 Output
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93 ------
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94
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95 GECCO will create the following files once done (using the same prefix as the input file):
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96
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97 - ``features.tsv``: The features file, containing the identified proteins and domains in the input sequences.
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98 - ``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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99 - ``{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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100
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101 Contact
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102 -------
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103
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104 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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105 `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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106 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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107
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108 ]]></help>
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109 <citations>
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110 <citation type="doi">10.1101/2021.05.03.442509</citation>
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111 </citations>
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112 </tool>