Mercurial > repos > bgruening > antismash
comparison antismash.xml @ 3:5784e268efca draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 19cbd26d33334a903a2028d463b2132cdd1f7e57"
author | bgruening |
---|---|
date | Sun, 09 Aug 2020 10:15:12 -0400 |
parents | 3f0077c88c16 |
children | e78e25d3b4bd |
comparison
equal
deleted
inserted
replaced
2:3f0077c88c16 | 3:5784e268efca |
---|---|
1 <?xml version='1.0' encoding='utf-8'?> | 1 <?xml version='1.0' encoding='utf-8'?> |
2 <tool id="antismash" name="Antismash" version="4.1" profile="17.01"> | 2 <tool id="antismash" name="Antismash" version="5.1.2" profile="17.01"> |
3 <description>allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters</description> | 3 <description>allows the genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters</description> |
4 <requirements> | 4 <requirements> |
5 <requirement type="package" version="4.1">antismash</requirement> | 5 <requirement type="package" version="5.1.2">antismash</requirement> |
6 </requirements> | 6 </requirements> |
7 <version_command>antismash --version</version_command> | 7 <version_command>antismash --version</version_command> |
8 <command detect_errors="aggressive"> | 8 <command detect_errors="aggressive"> |
9 <![CDATA[ | 9 <![CDATA[ |
10 export PYTHONWARNINGS="ignore::FutureWarning" && | |
11 | |
10 #import os, glob | 12 #import os, glob |
11 #set $htmloutputfolder = $html.files_path | 13 #set $htmloutputfolder = $html.files_path |
12 #if str($infile.ext) == 'genbank': | 14 #if str($infile.ext) == 'genbank': |
13 #set $file_extension = 'gb' | 15 #set $file_extension = 'gb' |
14 #else: | 16 #else: |
16 #end if | 18 #end if |
17 | 19 |
18 ln -s '$infile' input_tempfile.$file_extension && | 20 ln -s '$infile' input_tempfile.$file_extension && |
19 | 21 |
20 ## create html folder | 22 ## create html folder |
21 mkdir -p $htmloutputfolder && | 23 mkdir -p '$htmloutputfolder' && |
22 | 24 |
23 antismash | 25 antismash |
24 --cpus "\${GALAXY_SLOTS:-12}" | 26 --cpus "\${GALAXY_SLOTS:-12}" |
25 --taxon '${taxon}' | 27 --taxon '${cond_taxon.taxon}' |
26 --input-type '${input_type}' | 28 |
27 | 29 --genefinding-tool $cond_taxon.genefinding_tool |
28 ${clusterblast} | 30 |
29 ${subclusterblast} | 31 ${cb_general} |
30 ${smcogs} | 32 ${cb_subclusters} |
31 ${inclusive} | 33 ${cb_knownclusters} |
32 ${borderpredict} | 34 ${smcog_trees} |
33 ${tta} | 35 --tta-threshold ${tta_threshold} |
34 ${asf} | 36 ${asf} |
35 ${full_hmmer} | 37 |
38 ${extra_cluster} | |
39 ${clusterhmmer} | |
40 ${fullhmmer} | |
41 #if $cond_taxon.taxon == 'fungi': | |
42 $cond_taxon.cassis | |
43 #end if | |
36 | 44 |
37 input_tempfile.$file_extension && | 45 input_tempfile.$file_extension && |
38 | 46 |
39 ## copy all content to html folder | 47 ## copy all content to html folder |
40 cp input_tempfile/index.html '${html}' 2> /dev/null && | 48 cp input_tempfile/index.html '${html}' 2> /dev/null && |
43 ]]> | 51 ]]> |
44 </command> | 52 </command> |
45 <inputs> | 53 <inputs> |
46 <param name="infile" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank,EMBL or FASTA format"/> | 54 <param name="infile" type="data" format="genbank,fasta,embl" label="Sequence file in GenBank,EMBL or FASTA format"/> |
47 | 55 |
48 <param argument="--taxon" type="select" label="Origin of DNA"> | 56 <conditional name="cond_taxon"> |
49 <option value="bacteria" selected="True">Bacteria</option> | 57 <param argument="--taxon" type="select" label="Origin of DNA"> |
50 <option value="fungi">Fungi</option> | 58 <option value="bacteria" selected="True">Bacteria</option> |
51 </param> | 59 <option value="fungi">Fungi</option> |
52 | 60 </param> |
53 <param argument="--input_type" type="select" label="Origin of DNA"> | 61 <when value="bacteria"> |
54 <option value="nucl" selected="True">Nucleotide</option> | 62 <param argument="--genefinding-tool" type="select" label="Specify algorithm used for gene finding" |
55 <option value="prot">Amino-acid</option> | 63 help="The 'error' option will raise an error if genefinding is attempted. The 'none' option will not run genefinding"> |
56 </param> | 64 <option value="prodigal" selected="True">Prodigal</option> |
57 | 65 <option value="prodigal-m">Prodigal Metagenomic/Anonymous</option> |
58 <param argument="--clusterblast" type="boolean" truevalue="--clusterblast" falsevalue="" checked="False" | 66 <option value="glimmerhmm">GlimmerHMM</option> |
67 <option value="none">None</option> | |
68 <option value="error">Error</option> | |
69 </param> | |
70 </when> | |
71 <when value="fungi"> | |
72 <param argument="--genefinding-tool" type="select" label="Specify algorithm used for gene finding" | |
73 help="The 'error' option will raise an error if genefinding is attempted. The 'none' option will not run genefinding"> | |
74 <option value="glimmerhmm">GlimmerHMM</option> | |
75 <option value="none">None</option> | |
76 <option value="error">Error</option> | |
77 </param> | |
78 <param argument="--cassis" type="boolean" truevalue="--cassis" falsevalue="" checked="False" | |
79 label="Motif based prediction of SM gene cluster regions" /> | |
80 </when> | |
81 </conditional> | |
82 | |
83 | |
84 <param argument="--cb-general" type="boolean" truevalue="--cb-general" falsevalue="" checked="False" | |
59 label="BLAST identified clusters against known clusters" | 85 label="BLAST identified clusters against known clusters" |
60 help="Compare identified clusters against a database of antiSMASH-predicted clusters." /> | 86 help="Compare identified clusters against a database of antiSMASH-predicted clusters." /> |
61 <param argument="--subclusterblast" type="boolean" truevalue="--subclusterblast" falsevalue="" checked="True" | 87 <param argument="--cb-subclusters" type="boolean" truevalue="--cb-subclusters" falsevalue="" checked="True" |
62 label="Subcluster BLAST analysis" | 88 label="Subcluster BLAST analysis" |
63 help="Compare identified clusters against known subclusters responsible for synthesising precursors." /> | 89 help="Compare identified clusters against known subclusters responsible for synthesising precursors." /> |
64 <param argument="--knownclusterblast" type="boolean" truevalue="--knownclusterblast" falsevalue="" checked="True" | 90 <param argument="--cb-knownclusters" type="boolean" truevalue="--cb-knownclusters" falsevalue="" checked="True" |
65 label="KnowCluster BLAST analysis" | 91 label="KnowCluster BLAST analysis" |
66 help="Compare identified clusters against known gene clusters from the MIBiG database."/> | 92 help="Compare identified clusters against known gene clusters from the MIBiG database."/> |
67 <param argument="--smcogs" type="boolean" checked="True" truevalue="--smcogs" falsevalue="" | 93 <param argument="--smcog-trees" type="boolean" checked="True" truevalue="--smcog-trees" falsevalue="" |
68 label="Analysis of secondary metabolism gene families (smCOGs)" | 94 label="Analysis of secondary metabolism gene families (smCOGs)" |
69 help="Look for sec. met. clusters of orthologous groups."/> | 95 help="Look for sec. met. clusters of orthologous groups."/> |
70 <param argument="--inclusive" type="boolean" truevalue="--inclusive" falsevalue="" checked="False" | |
71 label="Inclusive ClusterFinder algorithm" | |
72 help="Use inclusive ClusterFinder algorithm for additional cluster detection."/> | |
73 <param argument="--borderpredict" type="boolean" truevalue="--borderpredict" falsevalue="" checked="False" | |
74 label="Predict gene cluster borders with ClusterFinder" | |
75 help="Use ClusterFinder algorithm to predict gene cluster borders."/> | |
76 <param argument="--asf" type="boolean" truevalue="--asf" falsevalue="" checked="True" | 96 <param argument="--asf" type="boolean" truevalue="--asf" falsevalue="" checked="True" |
77 label="Run active site finder module" /> | 97 label="Run active site finder analysus" /> |
78 <param argument="--tta" type="boolean" truevalue="--tta" falsevalue="" checked="False" | 98 <param argument="-pfam2go" type="boolean" truevalue="-pfam2go" falsevalue="" checked="True" |
79 label="Run TTA codon detection module" /> | 99 label="Run Pfam to Gene Ontology mapping module" /> |
80 <param argument="--full_hmmer" type="boolean" truevalue="--full-hmmer" falsevalue="" checked="False" | 100 <param argument="--tta-threshold" type="float" value="0.65" label="Lowest GC content to annotate TTA codons at" /> |
81 label="Run a whole-genome Pfam analysis" /> | 101 |
102 <param argument="--clusterhmmer" type="boolean" truevalue="--clusterhmmer" falsevalue="" checked="False" | |
103 label="Run a cluster-limited HMMer analysis" /> | |
104 <param argument="--fullhmmer" type="boolean" truevalue="--fullhmmer" falsevalue="" checked="False" | |
105 label="Run a whole-genome HMMer analysis" /> | |
106 | |
107 <param name="extra_cluster" type="select" label="Clusters"> | |
108 <option value="--cf-create-clusters" selected="True">Find extra clusters</option> | |
109 <option value="--cf-borders-only">Only annotate borders of existing clusters</option> | |
110 </param> | |
82 | 111 |
83 <param name="outputs" type="select" multiple="true" label="Outputs"> | 112 <param name="outputs" type="select" multiple="true" label="Outputs"> |
84 <option value="html" selected="True">HTML file</option> | 113 <option value="html" selected="True">HTML file</option> |
85 <option value="all">All results</option> | 114 <option value="all">All results</option> |
86 <option value="embl">EMBL files</option> | 115 <option value="embl">EMBL files</option> |
114 <output name="html" file="index.html"/> | 143 <output name="html" file="index.html"/> |
115 </test> | 144 </test> |
116 <test> | 145 <test> |
117 <param name="infile" value="sequence.gb"/> | 146 <param name="infile" value="sequence.gb"/> |
118 <param name="outputs" value="html,gb"/> | 147 <param name="outputs" value="html,gb"/> |
148 <param name="taxon" value="fungi"/> | |
149 <param name="clusterhmmer" value="True"/> | |
150 <param name="fullhmmer" value="True"/> | |
151 <param name="extra_cluster" value="--cf-create-clusters"/> | |
152 <param name="cassis" value="True"/> | |
153 <param name="cb_general" value="True"/> | |
119 <output_collection name="genbank" type="list"> | 154 <output_collection name="genbank" type="list"> |
120 <element name="ARBH01000003.1.cluster001" file="ARBH01000003.1.cluster001" ftype="genbank" compare="sim_size" /> | 155 <element name="ARBH01000003.1.cluster001" file="ARBH01000003.1.cluster001" ftype="genbank" /> |
121 <element name="ARBH01000003.1.final" file="ARBH01000003.1.final" ftype="genbank"/> | 156 <element name="ARBH01000003.1.final" file="ARBH01000003.1.final" ftype="genbank"/> |
122 </output_collection> | 157 </output_collection> |
123 <output name="html" file="index.2.html"/> | 158 <output name="html" file="index.2.html"/> |
124 </test> | 159 </test> |
125 </tests> | 160 </tests> |