Mercurial > repos > bgruening > antismash
comparison antismash.xml @ 25:99435bb90725 draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 18 Oct 2013 03:35:17 -0400 |
| parents | b942dfd80819 |
| children | a5eb6fad2a76 |
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| 24:b942dfd80819 | 25:99435bb90725 |
|---|---|
| 1 <tool id="antismash" name="Secondary Metabolites" version="2.0.2.1"> | 1 <tool id="antismash" name="Secondary Metabolites" version="2.0.2.1"> |
| 2 <description>and Antibiotics Analysis (antiSMASH)</description> | 2 <description>and Antibiotics Analysis (antiSMASH)</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="3.0">hmmer</requirement> | 4 <requirement type="package" version="3.0">hmmer</requirement> |
| 5 <requirement type="package">hmmer</requirement> | |
| 5 <requirement type="package" version="2.2.28">blast+</requirement> | 6 <requirement type="package" version="2.2.28">blast+</requirement> |
| 7 <requirement type="package">blast+</requirement> | |
| 6 <requirement type="package" version="3.8.31">muscle</requirement> | 8 <requirement type="package" version="3.8.31">muscle</requirement> |
| 9 <requirement type="package">muscle</requirement> | |
| 7 <requirement type="package" version="1.4.0-post-1">straight.plugin</requirement> | 10 <requirement type="package" version="1.4.0-post-1">straight.plugin</requirement> |
| 8 <requirement type="package" version="1.62">biopython</requirement> | 11 <requirement type="package" version="1.62">biopython</requirement> |
| 9 <requirement type="package" version="1.2.6">pyquery</requirement> | 12 <requirement type="package" version="1.2.6">pyquery</requirement> |
| 10 <requirement type="package" version="0.1.2">helperlibs</requirement> | 13 <requirement type="package" version="0.1.2">helperlibs</requirement> |
| 11 <requirement type="package" version="0.9">cssselect</requirement> | 14 <requirement type="package" version="0.9">cssselect</requirement> |
| 12 <requirement type="package" version="2.0.2">antismash</requirement> | 15 <requirement type="package" version="2.0.2">antismash</requirement> |
| 16 <requirement type="package">antismash</requirement> | |
| 13 </requirements> | 17 </requirements> |
| 14 <command> | 18 <command> |
| 15 #import os, glob | 19 #import os, glob |
| 16 #set $outputfolder = $html.files_path | 20 #set $outputfolder = $html.files_path |
| 17 #if str($infile.ext) == 'genbank': | 21 #if str($infile.ext) == 'genbank': |
| 22 #end if | 26 #end if |
| 23 | 27 |
| 24 ln -s $infile #echo 'input_tempfile.' + $file_extension#; | 28 ln -s $infile #echo 'input_tempfile.' + $file_extension#; |
| 25 mkdir -p $outputfolder; | 29 mkdir -p $outputfolder; |
| 26 run_antismash.py | 30 run_antismash.py |
| 27 --cpus 4 | 31 --cpus 12 |
| 28 --enable $types | 32 --enable $types |
| 29 --input-type 'nucl' | 33 --input-type 'nucl' |
| 30 $smcogs | 34 $smcogs |
| 31 $clusterblast | 35 $clusterblast |
| 32 $subclusterblast | 36 $subclusterblast |
| 33 $inclusive | 37 $inclusive |
| 34 $full_hmmer | 38 $full_hmmer |
| 35 $full_blast | 39 $full_blast |
| 40 $eukaryotic | |
| 41 | |
| 36 | 42 |
| 37 #if str($pfam_database) != "None": | 43 #if str($pfam_database) != "None": |
| 38 --pfamdir $pfam_database.fields.path | 44 --pfamdir $pfam_database.fields.path |
| 39 #end if | 45 #end if |
| 40 | 46 |
| 47 --debug | |
| 48 | |
| 41 --disable-embl | 49 --disable-embl |
| 42 --outputfolder $outputfolder | 50 --outputfolder $outputfolder |
| 43 | 51 |
| 44 #echo 'input_tempfile.' + $file_extension# | 52 #echo 'input_tempfile.' + $file_extension# |
| 45 | 53 |
| 46 ## leave out the start and end features, it can be easily replaced with Galaxy tools | 54 ## leave out the start and end features, it can be easily replaced with Galaxy tools |
| 47 ##--from START Start analysis at nucleotide specified | 55 ##--from START Start analysis at nucleotide specified |
| 48 ##--to END | 56 ##--to END |
| 49 | 57 |
| 58 2>&1 | |
| 59 | |
| 60 ## | |
| 61 ## shuffling files to create the correct outputs for Galaxy | |
| 62 ## | |
| 63 | |
| 64 ## html output | |
| 50 ; | 65 ; |
| 51 ## shuffling files to create the correct outputs for Galaxy | 66 cp #echo os.path.join($outputfolder, 'index.html')# $html 2> /dev/null |
| 52 | |
| 53 ## html output | |
| 54 #if 'html' in str($outputs).split(','): | |
| 55 cp #echo os.path.join($outputfolder, 'index.html')# $html 2>/dev/null; | |
| 56 #end if | |
| 57 | 67 |
| 58 ## gene clusters | 68 ## gene clusters |
| 59 #if 'geneclusterprots_tabular' in str($outputs).split(','): | 69 #if 'geneclusterprots_tabular' in str($outputs).split(','): |
| 60 cp #echo os.path.join($outputfolder, 'geneclusters.txt')# $geneclusterprots_tabular 2>/dev/null; | 70 ; |
| 71 cp #echo os.path.join($outputfolder, 'geneclusters.txt')# $geneclusterprots_tabular 2> /dev/null | |
| 61 #end if | 72 #end if |
| 62 | 73 |
| 63 #if 'geneclusterprots_fasta' in str($outputs).split(','): | 74 #if 'geneclusterprots_fasta' in str($outputs).split(','): |
| 64 cp #echo os.path.join($outputfolder, '*_genecluster_proteins.fa')# $geneclusterprots_fasta 2>/dev/null; | 75 ; |
| 76 cp #echo os.path.join($outputfolder, '*_genecluster_proteins.fa')# $geneclusterprots_fasta 2> /dev/null | |
| 65 #end if | 77 #end if |
| 66 | 78 |
| 67 | 79 |
| 68 ##SVG images | 80 ##SVG images |
| 69 #if 'archive_svgs' in str($outputs).split(','): | 81 #if 'archive_svgs' in str($outputs).split(','): |
| 70 cd #echo os.path.join($outputfolder, 'svg')#; | 82 ; |
| 83 cd #echo os.path.join($outputfolder, 'svg')# | |
| 71 #if $clusterblast: | 84 #if $clusterblast: |
| 72 tar cfz $archive_svgs *_all.svg genecluster* 2>/dev/null; | 85 ; |
| 86 tar cfz $archive_svgs *_all.svg genecluster* 2> /dev/null | |
| 73 #else: | 87 #else: |
| 74 tar cfz $archive_svgs genecluster*; | 88 ; |
| 89 tar cfz $archive_svgs genecluster* | |
| 75 #end if | 90 #end if |
| 76 #end if | 91 #end if |
| 77 | 92 |
| 78 ##all files in a archive | 93 ##all files in a archive |
| 79 #if 'archive' in str($outputs).split(','): | 94 #if 'archive' in str($outputs).split(','): |
| 95 ; | |
| 80 cd $outputfolder; | 96 cd $outputfolder; |
| 81 tar cf $archive *.zip 2>/dev/null; | 97 tar cf $archive *.zip 2> /dev/null |
| 82 #end if | 98 #end if |
| 83 | 99 |
| 84 ## genbank | 100 ## genbank |
| 85 #if 'gb' in str($outputs).split(','): | 101 #if 'gb' in str($outputs).split(','): |
| 86 cat #echo os.path.join($outputfolder, '*.gbk')# > $genbank 2>/dev/null; | 102 ; |
| 103 cat #echo os.path.join($outputfolder, '*.gbk')# > $genbank 2> /dev/null | |
| 87 #end if | 104 #end if |
| 88 | 105 |
| 89 </command> | 106 </command> |
| 90 <inputs> | 107 <inputs> |
| 91 <param name="infile" type="data" format="genbank" label="Nucleotide sequence file in GenBank format"/> | 108 <param name="infile" type="data" format="genbank" label="Nucleotide sequence file in GenBank format"/> |
| 109 | |
| 110 <param name="eukaryotic" type="select" label="Origin of DNA"> | |
| 111 <option value="" selected="True">Prokaryotic</option> | |
| 112 <option value="--eukaryotic">Eukaryotic</option> | |
| 113 </param> | |
| 92 | 114 |
| 93 <param name="clusterblast" type="boolean" label="BLAST identified clusters against known clusters" | 115 <param name="clusterblast" type="boolean" label="BLAST identified clusters against known clusters" |
| 94 help="(--clusterblast)" | 116 help="(--clusterblast)" |
| 95 truevalue="--clusterblast" falsevalue="" checked="True" /> | 117 truevalue="--clusterblast" falsevalue="" checked="True" /> |
| 96 <param name="subclusterblast" type="boolean" label="Subcluster BLAST analysis" | 118 <param name="subclusterblast" type="boolean" label="Subcluster BLAST analysis" |
| 144 <option value="phenazine" selected="True">phenazines</option> | 166 <option value="phenazine" selected="True">phenazines</option> |
| 145 <option value="phosphonate" selected="True">phosphonates</option> | 167 <option value="phosphonate" selected="True">phosphonates</option> |
| 146 <option value="other" selected="True">others</option> | 168 <option value="other" selected="True">others</option> |
| 147 </param> | 169 </param> |
| 148 | 170 |
| 149 <param name="outputs" type="select" multiple="true" label="Output formats"> | 171 <param name="outputs" type="select" multiple="true" label="Additional outputs"> |
| 150 <option value="geneclusterprots_fasta" selected="True">Gene cluster proteins (FASTA)</option> | 172 <option value="geneclusterprots_fasta" selected="True">Gene cluster proteins (FASTA)</option> |
| 151 <option value="geneclusterprots_tabular">Gene cluster proteins (Tabular)</option> | 173 <option value="geneclusterprots_tabular">Gene cluster proteins (Tabular)</option> |
| 152 <option value="html" selected="True">Interactive summary page (html)</option> | |
| 153 <option value="archive_svgs">All clusters as image (compressed)</option> | 174 <option value="archive_svgs">All clusters as image (compressed)</option> |
| 154 <option value="archive">All files compressed</option> | 175 <option value="archive">All files compressed</option> |
| 155 <option value="gb">Annotated genome (GenBank)</option> | 176 <option value="gb">Annotated genome (GenBank)</option> |
| 156 </param> | 177 </param> |
| 157 | 178 |
| 168 </data> | 189 </data> |
| 169 <data format="tar.gz" name="archive_svgs" label="${tool.name} on ${on_string} (SVG images)"> | 190 <data format="tar.gz" name="archive_svgs" label="${tool.name} on ${on_string} (SVG images)"> |
| 170 <filter>'archive_svgs' in outputs</filter> | 191 <filter>'archive_svgs' in outputs</filter> |
| 171 </data> | 192 </data> |
| 172 <data format="html" name="html" label="${tool.name} on ${on_string} (html report)"> | 193 <data format="html" name="html" label="${tool.name} on ${on_string} (html report)"> |
| 194 <!-- html is default output at any time. | |
| 173 <filter>'html' in outputs</filter> | 195 <filter>'html' in outputs</filter> |
| 196 --> | |
| 174 </data> | 197 </data> |
| 175 <data name="genbank" format="genbank" label="${tool.name} on ${on_string} (genbank)"> | 198 <data name="genbank" format="genbank" label="${tool.name} on ${on_string} (genbank)"> |
| 176 <filter>'gb' in outputs</filter> | 199 <filter>'gb' in outputs</filter> |
| 177 </data> | 200 </data> |
| 178 </outputs> | 201 </outputs> |
| 215 Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, | 238 Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, |
| 216 Rainer Breitling and Eriko Takano (2011). antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research, doi: 10.1093/nar/gkr466. | 239 Rainer Breitling and Eriko Takano (2011). antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research, doi: 10.1093/nar/gkr466. |
| 217 | 240 |
| 218 http://antismash.secondarymetabolites.org/help.html | 241 http://antismash.secondarymetabolites.org/help.html |
| 219 | 242 |
| 243 | |
| 244 Bjoern A. Gruening: https://github.com/bgruening/galaxytools/tree/master/antismash | |
| 245 | |
| 220 </help> | 246 </help> |
| 221 </tool> | 247 </tool> |