Mercurial > repos > althonos > gecco

comparison gecco.xml @ 19:cc91d730cc4f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fix syntax of Galaxy script for GECCO
author althonos
date Mon, 16 Jan 2023 18:35:56 +0000
parents 56b924f62165
children 64b724dd8d04
comparison
equal deleted inserted replaced
18:3dd71eaa2909 19:cc91d730cc4f
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool id="gecco" name="GECCO" version="0.9.1" python_template_version="3.5"> 2 <tool id="gecco" name="GECCO" version="0.9.6" python_template_version="3.5">
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> 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>
4 <creator>
5 <organization name="Zeller Team" url="https://www.embl.org/groups/zeller/"/>
6 </creator>
7 <edam_topics>
8 <edam_topic>topic_0080</edam_topic>
9 </edam_topics>
10 <edam_operations>
11 <edam_operation>operation_0415</edam_operation>
12 </edam_operations>
4 <requirements> 13 <requirements>
5 <requirement type="package" version="0.9.1">gecco</requirement> 14 <requirement type="package" version="0.9.6">gecco</requirement>
6 </requirements> 15 </requirements>
7 <version_command>gecco --version</version_command> 16 <version_command>gecco --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[ 17 <command detect_errors="aggressive"><![CDATA[
9 18
10 #if str($input.ext) == 'genbank': 19 #if str($input.ext) == 'genbank':
32 --threshold $threshold 41 --threshold $threshold
33 #end if 42 #end if
34 #if $antismash_sideload: 43 #if $antismash_sideload:
35 --antismash-sideload 44 --antismash-sideload
36 #end if 45 #end if
46 #unless $pad:
47 --no-pad
48 #end unless
37 49
38 && mv input_tempfile.genes.tsv '$genes' 50 && mv input_tempfile.genes.tsv '$genes'
39 && mv input_tempfile.features.tsv '$features' 51 && mv input_tempfile.features.tsv '$features'
40 && mv input_tempfile.clusters.tsv '$clusters' 52 && mv input_tempfile.clusters.tsv '$clusters'
41 #if $antismash_sideload 53 #if $antismash_sideload
44 56
45 ]]></command> 57 ]]></command>
46 <inputs> 58 <inputs>
47 <param name="input" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank, EMBL or FASTA format"/> 59 <param name="input" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank, EMBL or FASTA format"/>
48 <param argument="--mask" type="boolean" checked="false" label="Enable masking of regions with unknown nucleotides when finding ORFs"/> 60 <param argument="--mask" type="boolean" checked="false" label="Enable masking of regions with unknown nucleotides when finding ORFs"/>
61 <param argument="--pad" type="boolean" checked="true" label="Enable padding of gene sequences smaller than the CRF window length"/>
49 <param argument="--cds" type="integer" min="0" value="" optional="true" label="Minimum number of genes required for a cluster"/> 62 <param argument="--cds" type="integer" min="0" value="" optional="true" label="Minimum number of genes required for a cluster"/>
50 <param argument="--threshold" type="float" min="0" max="1" value="" optional="true" label="Probability threshold for cluster detection"/> 63 <param argument="--threshold" type="float" min="0" max="1" value="" optional="true" label="Probability threshold for cluster detection"/>
51 <param argument="--postproc" type="select" label="Post-processing method for gene cluster validation"> 64 <param argument="--postproc" type="select" label="Post-processing method for gene cluster validation">
52 <option value="antismash">antiSMASH</option> 65 <option value="antismash">antiSMASH</option>
53 <option value="gecco" selected="true">GECCO</option> 66 <option value="gecco" selected="true">GECCO</option>
70 <test> 83 <test>
71 <param name="input" value="BGC0001866.fna"/> 84 <param name="input" value="BGC0001866.fna"/>
72 <output name="features" file="features.tsv"/> 85 <output name="features" file="features.tsv"/>
73 <output name="genes" file="genes.tsv"/> 86 <output name="genes" file="genes.tsv"/>
74 <output name="clusters" file="clusters.tsv"/> 87 <output name="clusters" file="clusters.tsv"/>
88 <param name="edge_distance" value="10"/>
75 </test> 89 </test>
76 <test> 90 <test>
77 <param name="input" value="BGC0001866.fna"/> 91 <param name="input" value="BGC0001866.fna"/>
78 <param name="edge_distance" value="0"/>
79 <output name="features" file="features.tsv"/> 92 <output name="features" file="features.tsv"/>
80 <output name="genes" file="genes.tsv"/> 93 <output name="genes" file="genes.tsv"/>
81 <output name="clusters" file="clusters.tsv"/> 94 <output name="clusters" file="clusters.tsv"/>
82 <output_collection name="records" type="list"> 95 <output_collection name="records" type="list">
83 <element name="BGC0001866.1_cluster_1" file="BGC0001866.1_cluster_1.gbk" ftype="genbank" compare="diff" lines_diff="4"/> 96 <element name="BGC0001866.1_cluster_1" file="BGC0001866.1_cluster_1.gbk" ftype="genbank" compare="diff" lines_diff="4"/>
84 </output_collection> 97 </output_collection>
85 </test> 98 </test>
86 <test> 99 <test>
87 <param name="input" value="BGC0001866.fna"/> 100 <param name="input" value="BGC0001866.fna"/>
88 <param name="antismash_sideload" value="True"/> 101 <param name="antismash_sideload" value="True"/>
89 <param name="edge_distance" value="0"/>
90 <output name="features" file="features.tsv"/> 102 <output name="features" file="features.tsv"/>
91 <output name="genes" file="genes.tsv"/> 103 <output name="genes" file="genes.tsv"/>
92 <output name="clusters" file="clusters.tsv"/> 104 <output name="clusters" file="clusters.tsv"/>
93 <output name="sideload" file="sideload.json"/> 105 <output name="sideload" file="sideload.json"/>
94 <output_collection name="records" type="list"> 106 <output_collection name="records" type="list">