gecco: gecco.xml annotate

annotate gecco.xml @ 10:9156eb4ee20c draft

"Release v0.9.1-alpha1"

author	althonos
date	Sun, 20 Mar 2022 15:44:07 +0000
parents	d64fe390f3c9
children	56b924f62165

rev	line source
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	1 <?xml version='1.0' encoding='utf-8'?>
9 d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	2 <tool id="gecco" name="GECCO" version="0.8.10" python_template_version="3.5">
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	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>
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	4 <requirements>
9 d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	5 <requirement type="package" version="0.8.10">gecco</requirement>
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	6 </requirements>
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	7 <version_command>gecco --version</version_command>
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	8 <command detect_errors="aggressive"><![CDATA[
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	9
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	10 #if str($input.ext) == 'genbank':
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	11 #set $file_extension = 'gbk'
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	12 #else:
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	13 #set $file_extension = $input.ext
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	14 #end if
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	15 ln -s '$input' input_tempfile.$file_extension &&
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	16
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	17 gecco -vv run
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	18 --format $input.ext
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	19 --genome input_tempfile.$file_extension
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	20 --postproc $postproc
9 d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	21 --edge-distance $edge_distance
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	22 --force-clusters-tsv
9 d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	23 #if $mask
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	24 --mask
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	25 #end if
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	26 #if $cds:
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	27 --cds $cds
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	28 #end if
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	29 #if $threshold:
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	30 --threshold $threshold
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	31 #end if
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	32 #if $antismash_sideload:
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	33 --antismash-sideload
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	34 #end if
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	35
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	36 && mv input_tempfile.features.tsv '$features'
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	37 && mv input_tempfile.clusters.tsv '$clusters'
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	38 #if $antismash_sideload
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	39 && mv input_tempfile.sideload.json '$sideload'
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	40 #end if
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	41
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	42 ]]></command>
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	43 <inputs>
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	44 <param name="input" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank, EMBL or FASTA format"/>
9 d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	45 <param argument="--mask" type="boolean" checked="false" label="Enable masking of regions with unknown nucleotides when finding ORFs"/>
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	46 <param argument="--cds" type="integer" min="0" value="" optional="true" label="Minimum number of genes required for a cluster"/>
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	47 <param argument="--threshold" type="float" min="0" max="1" value="" optional="true" label="Probability threshold for cluster detection"/>
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	48 <param argument="--postproc" type="select" label="Post-processing method for gene cluster validation">
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	49 <option value="antismash">antiSMASH</option>
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	50 <option value="gecco" selected="true">GECCO</option>
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	51 </param>
9 d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	52 <param argument="--edge-distance" type="integer" min="0" value="10" label="Number of genes from the contig edges to filter out"/>
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	53 <param argument="--antismash-sideload" type="boolean" checked="false" label="Generate an antiSMASH v6 sideload JSON file"/>
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	54 </inputs>
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	55 <outputs>
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	56 <collection name="records" type="list" label="${tool.name} detected Biosynthetic Gene Clusters on ${on_string} (GenBank)">
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	57 <discover_datasets pattern="(?P<designation>.*)\.gbk" ext="genbank" visible="false" />
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	58 </collection>
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	59 <data name="features" format="tabular" label="${tool.name} summary of detected features on ${on_string} (TSV)"/>
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	60 <data name="clusters" format="tabular" label="${tool.name} summary of detected BGCs on ${on_string} (TSV)"/>
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	61 <data name="sideload" format="json" label="antiSMASH v6 sideload file with ${tool.name} detected BGCs on ${on_string} (JSON)">
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	62 <filter>antismash_sideload</filter>
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	63 </data>
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	64 </outputs>
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	65 <tests>
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	66 <test>
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	67 <param name="input" value="BGC0001866.fna"/>
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	68 <output name="features" file="features.tsv"/>
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	69 <output name="clusters" file="clusters.tsv"/>
9 d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	70 </test>
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	71 <test>
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	72 <param name="input" value="BGC0001866.fna"/>
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	73 <param name="edge_distance" value="0"/>
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	74 <output name="features" file="features.tsv"/>
d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	75 <output name="clusters" file="clusters.tsv"/>
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	76 <output_collection name="records" type="list">
4 88dc16b4f583 "Fix number of allowed different lines in `galaxy/gecco.xml` tests" althonos parents: 3 diff changeset	77 <element name="BGC0001866.1_cluster_1" file="BGC0001866.1_cluster_1.gbk" ftype="genbank" compare="diff" lines_diff="4"/>
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	78 </output_collection>
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	79 </test>
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	80 <test>
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	81 <param name="input" value="BGC0001866.fna"/>
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	82 <param name="antismash_sideload" value="True"/>
9 d64fe390f3c9 "Fix test files used in Galaxy test workflow" althonos parents: 4 diff changeset	83 <param name="edge_distance" value="0"/>
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	84 <output name="features" file="features.tsv"/>
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	85 <output name="clusters" file="clusters.tsv"/>
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	86 <output name="sideload" file="sideload.json"/>
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	87 <output_collection name="records" type="list">
4 88dc16b4f583 "Fix number of allowed different lines in `galaxy/gecco.xml` tests" althonos parents: 3 diff changeset	88 <element name="BGC0001866.1_cluster_1" file="BGC0001866.1_cluster_1.gbk" ftype="genbank" compare="diff" lines_diff="4"/>
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	89 </output_collection>
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	90 </test>
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	91 </tests>
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	92 <help><![CDATA[
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	93
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	94 Overview
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	95 --------
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	96
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	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).
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	98 It is developed in the Zeller group and is part of the suite of computational microbiome analysis tools hosted at EMBL.
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	99
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	100 Input
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	101 -----
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	102
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	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.
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	104
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	105 Output
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	106 ------
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	107
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	108 GECCO will create the following files once done (using the same prefix as the input file):
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	109
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	110 - ``features.tsv``: The features file, containing the identified proteins and domains in the input sequences.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	111 - ``clusters.tsv``: If any were found, a clusters file, containing the coordinates of the predicted clusters, along their putative biosynthetic type.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	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.
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	113
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	114 Contact
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	115 -------
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	116
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	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
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	118 `GitHub repository <https://github.com/zellerlab/gecco>`_. You can also directly contact `Martin Larralde via email <mailto:martin.larralde@embl.de>`_.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	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.
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	120
359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	121 ]]></help>
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	122 <citations>
3 359232b58f6a "Update Galaxy tool wrapper to follow the IUC best practices" althonos parents: 0 diff changeset	123 <citation type="doi">10.1101/2021.05.03.442509</citation>
0 1625927fc16f "Release v0.8.4" althonos parents: diff changeset	124 </citations>
1625927fc16f "Release v0.8.4" althonos parents: diff changeset	125 </tool>

Mercurial > repos > althonos > gecco

annotate gecco.xml @ 10:9156eb4ee20c draft