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comparison antismash.xml @ 3:5784e268efca draft

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"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
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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>