Mercurial > repos > althonos > gecco
comparison gecco.xml @ 9:d64fe390f3c9 draft
"Fix test files used in Galaxy test workflow"
author | althonos |
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date | Thu, 24 Feb 2022 16:35:48 +0000 |
parents | 88dc16b4f583 |
children | 56b924f62165 |
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8:cebc53d02da6 | 9:d64fe390f3c9 |
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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<designation>.*)\.gbk" ext="genbank" visible="false" /> | 57 <discover_datasets pattern="(?P<designation>.*)\.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"/> |