Mercurial > repos > althonos > gecco

comparison gecco.xml @ 9:d64fe390f3c9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"Fix test files used in Galaxy test workflow"
author althonos
date Thu, 24 Feb 2022 16:35:48 +0000
parents 88dc16b4f583
children 56b924f62165
comparison
equal deleted inserted replaced
8:cebc53d02da6 9:d64fe390f3c9
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <tool id="gecco" name="GECCO" version="0.8.5" python_template_version="3.5"> 2 <tool id="gecco" name="GECCO" version="0.8.10" 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 <requirements> 4 <requirements>
5 <requirement type="package" version="0.8.5">gecco</requirement> 5 <requirement type="package" version="0.8.10">gecco</requirement>
6 </requirements> 6 </requirements>
7 <version_command>gecco --version</version_command> 7 <version_command>gecco --version</version_command>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 9
10 #if str($input.ext) == 'genbank': 10 #if str($input.ext) == 'genbank':
16 16
17 gecco -vv run 17 gecco -vv run
18 --format $input.ext 18 --format $input.ext
19 --genome input_tempfile.$file_extension 19 --genome input_tempfile.$file_extension
20 --postproc $postproc 20 --postproc $postproc
21 --edge-distance $edge_distance
21 --force-clusters-tsv 22 --force-clusters-tsv
23 #if $mask
24 --mask
25 #end if
22 #if $cds: 26 #if $cds:
23 --cds $cds 27 --cds $cds
24 #end if 28 #end if
25 #if $threshold: 29 #if $threshold:
26 --threshold $threshold 30 --threshold $threshold
36 #end if 40 #end if
37 41
38 ]]></command> 42 ]]></command>
39 <inputs> 43 <inputs>
40 <param name="input" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank, EMBL or FASTA format"/> 44 <param name="input" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank, EMBL or FASTA format"/>
45 <param argument="--mask" type="boolean" checked="false" label="Enable masking of regions with unknown nucleotides when finding ORFs"/>
41 <param argument="--cds" type="integer" min="0" value="" optional="true" label="Minimum number of genes required for a cluster"/> 46 <param argument="--cds" type="integer" min="0" value="" optional="true" label="Minimum number of genes required for a cluster"/>
42 <param argument="--threshold" type="float" min="0" max="1" value="" optional="true" label="Probability threshold for cluster detection"/> 47 <param argument="--threshold" type="float" min="0" max="1" value="" optional="true" label="Probability threshold for cluster detection"/>
43 <param argument="--postproc" type="select" label="Post-processing method for gene cluster validation"> 48 <param argument="--postproc" type="select" label="Post-processing method for gene cluster validation">
44 <option value="antismash">antiSMASH</option> 49 <option value="antismash">antiSMASH</option>
45 <option value="gecco" selected="true">GECCO</option> 50 <option value="gecco" selected="true">GECCO</option>
46 </param> 51 </param>
52 <param argument="--edge-distance" type="integer" min="0" value="10" label="Number of genes from the contig edges to filter out"/>
47 <param argument="--antismash-sideload" type="boolean" checked="false" label="Generate an antiSMASH v6 sideload JSON file"/> 53 <param argument="--antismash-sideload" type="boolean" checked="false" label="Generate an antiSMASH v6 sideload JSON file"/>
48 </inputs> 54 </inputs>
49 <outputs> 55 <outputs>
50 <collection name="records" type="list" label="${tool.name} detected Biosynthetic Gene Clusters on ${on_string} (GenBank)"> 56 <collection name="records" type="list" label="${tool.name} detected Biosynthetic Gene Clusters on ${on_string} (GenBank)">
51 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gbk" ext="genbank" visible="false" /> 57 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.gbk" ext="genbank" visible="false" />
59 <tests> 65 <tests>
60 <test> 66 <test>
61 <param name="input" value="BGC0001866.fna"/> 67 <param name="input" value="BGC0001866.fna"/>
62 <output name="features" file="features.tsv"/> 68 <output name="features" file="features.tsv"/>
63 <output name="clusters" file="clusters.tsv"/> 69 <output name="clusters" file="clusters.tsv"/>
70 </test>
71 <test>
72 <param name="input" value="BGC0001866.fna"/>
73 <param name="edge_distance" value="0"/>
74 <output name="features" file="features.tsv"/>
75 <output name="clusters" file="clusters.tsv"/>
64 <output_collection name="records" type="list"> 76 <output_collection name="records" type="list">
65 <element name="BGC0001866.1_cluster_1" file="BGC0001866.1_cluster_1.gbk" ftype="genbank" compare="diff" lines_diff="4"/> 77 <element name="BGC0001866.1_cluster_1" file="BGC0001866.1_cluster_1.gbk" ftype="genbank" compare="diff" lines_diff="4"/>
66 </output_collection> 78 </output_collection>
67 </test> 79 </test>
68 <test> 80 <test>
69 <param name="input" value="BGC0001866.fna"/> 81 <param name="input" value="BGC0001866.fna"/>
70 <param name="antismash_sideload" value="True"/> 82 <param name="antismash_sideload" value="True"/>
83 <param name="edge_distance" value="0"/>
71 <output name="features" file="features.tsv"/> 84 <output name="features" file="features.tsv"/>
72 <output name="clusters" file="clusters.tsv"/> 85 <output name="clusters" file="clusters.tsv"/>
73 <output name="sideload" file="sideload.json"/> 86 <output name="sideload" file="sideload.json"/>
74 <output_collection name="records" type="list"> 87 <output_collection name="records" type="list">
75 <element name="BGC0001866.1_cluster_1" file="BGC0001866.1_cluster_1.gbk" ftype="genbank" compare="diff" lines_diff="4"/> 88 <element name="BGC0001866.1_cluster_1" file="BGC0001866.1_cluster_1.gbk" ftype="genbank" compare="diff" lines_diff="4"/>