Mercurial > repos > bgruening > antismash
changeset 0:7ad005dfbe78 draft
Uploaded
| author | bgruening |
|---|---|
| date | Fri, 04 Oct 2013 03:33:05 -0400 |
| parents | |
| children | abd9e69bb886 |
| files | antismash.xml readme.txt tool_dependencies.xml |
| diffstat | 3 files changed, 261 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/antismash.xml Fri Oct 04 03:33:05 2013 -0400 @@ -0,0 +1,123 @@ +<tool id="antismash" name="Secondary Metabolites" version="2.0.2.0"> + <description>and Antibiotics Analysis (antiSMASH)</description> + <command>run_antismash.py + + --input $infile + --cpus 4 + #set $type_list = ','.join([$type for $type in $types]) + --enable $type_list + --input-type nucl + $smcogs + $clusterblast + $subclusterblast + $inclusive + $full_hmmer + $full_blast + + + ##--from START Start analysis at nucleotide specified + ##--to END + + </command> + <inputs> + <param name="infile" type="data" format="gb,embl" label="Nucleotide sequence file in GenBank or EMBL format"/> + + <param name="smcogs" type="boolean" label="Look for sec.met. clusters of orthologous groups" falsevalue="" truevalue="--smcogs" checked="false" /> + <param name="clusterblast" type="boolean" label="BLAST identified clusters against known clusters" truevalue="--clusterblast" falsevalue="" checked="false" /> + <param name="subclusterblast" type="boolean" label="BLAST identified clusters against known subclusters" truevalue="--subclusterblast" falsevalue="" checked="false" /> + + <param name="inclusive" type="boolean" label="Use inclusive algorithm for cluster detection" truevalue="--inclusive" falsevalue="" checked="false" /> + <param name="full_hmmer" type="boolean" label="Run a whole-genome HMMer analysis" truevalue="--full-hmmer" falsevalue="" checked="false" /> + <param name="full_blast" type="boolean" label="Run a whole-genome BLAST analysis" truevalue="--full-blast" falsevalue="" checked="false" /> + + <param name="types" type="select" display="checkboxes" multiple="true" label="Gene cluster types to search"> + <option value="1" selected="True">all</option> + <option value="2">type I polyketide synthases</option> + <option value="3">type II polyketide synthases</option> + <option value="4">type III polyketide synthases</option> + <option value="5">nonribosomal peptide synthetases</option> + <option value="6">terpene synthases</option> + <option value="7">lantibiotics</option> + <option value="8">bacteriocins</option> + <option value="9">beta-lactams</option> + <option value="10">aminoglycosides / aminocyclitols</option> + <option value="11">aminocoumarins</option> + <option value="12">siderophores</option> + <option value="13">ectoines</option> + <option value="14">butyrolactones</option> + <option value="15">indoles</option> + <option value="16">nucleosides</option> + <option value="17">phosphoglycolipids</option> + <option value="18">melanins</option> + <option value="19">others</option> + </param> + +<!-- +t1pks (PKS_KS & PKS_AT) or (ene_KS & PKS_AT) or (mod_KS & PKS_AT) or (hyb_KS & PKS_AT) or (itr_KS & PKS_AT) or (tra_KS & PKS_AT) 20 20 +transatpks (PKS_KS & ATd) or (ene_KS & ATd) or (mod_KS & ATd) or (hyb_KS & ATd) or (itr_KS & ATd) or (tra_KS & ATd) 20 20 +t2pks t2ks or t2clf or t2pks2 20 20 +t3pks Chal_sti_synt_C or Chal_sti_synt_N 20 20 +t4pks hglE or hglD 20 20 +nrps (Condensation & AMP-binding) or (Condensation & A-OX) or cluster(Condensation,AMP-binding) 20 20 +terpene Terpene_Synth or Terpene_synth_C or phytoene_synt or Lycopene_cycl or terpene_cyclase or NapT7 or fung_ggpps or fung_ggpps2 or dmat or trichodiene_synth 20 10 +lantipeptide (Lant_dehyd_N & Lant_dehyd_C) or cluster(LANC_like,Flavoprotein) or cluster(LANC_like,Trp_halogenase) or cluster(LANC_like,p450) or (LANC_like & Pkinase) or (LANC_like & DUF4135) or cluster(LANC_like,Lant_dehyd_N) or cluster(LANC_like,Lant_dehyd_C) or cluster(LANC_like,adh_short) or cluster(LANC_like,adh_short_C2) or TIGR03731 or Antimicr18 or Gallidermin or L_biotic_A or TIGR03731 or leader_d or leader_eh or leader_abc or mature_d or mature_ab or mature_a or mature_b or mature_ha or mature_h_beta or lacticin_l or lacticin_mat or LD_lanti_pre or strep_PEQAXS 20 10 +bacteriocin strepbact or Antimicrobial14 or Bacteriocin_IId or BacteriocIIc_cy or Bacteriocin_II or Bacteriocin_IIi or Lactococcin or Antimicrobial17 or Lactococcin_972 or Bacteriocin_IIc or LcnG-beta or Bacteriocin_Iii or Subtilosin_A or Cloacin or Linocin_M18 or TIGR03603 or TIGR03604 or TIGR03605 or TIGR03651 or TIGR03678 or TIGR03693 or TIGR03798 or TIGR03882 or TIGR03601 or TIGR03602 or TIGR03795 or TIGR03793 or TIGR03975 or mvnA or thiostrepton or subtilosin or cypemycin or mvd or lasso or DUF692 or micJ25 or mcjC or glycocin or botH or skfc or thuricin or sublancin 20 5 +blactam BLS or CAS or tabtoxin 20 10 +amglyccycl strH or strK1 or strK2 or NeoL or DOIS or ValA or SpcFG or SpcDK_glyc or salQ 20 10 +aminocoumarin novK or novJ or novI or novH or SpcDK_cou 20 10 +siderophore IucA_IucC 20 5 +ectoine ectoine_synt 20 5 +butyrolactone AfsA 20 5 +indole indsynth 20 10 +nucleoside LipM or LipU or LipV or LipU or ToyB or TunD or pur6 or pur10 or nikJ or nikO 20 10 +phosphoglycolipid MoeO5 or moeGT 20 10 +melanin melC 20 5 +oligosaccharide minimum(3,[Glycos_transf_1,Glycos_transf_2,Glyco_transf_28,MGT,MGT2,DUF1205], [MGT2]) 20 10 +furan mmyO 20 5 +hserlactone Autoind_synth 20 10 +thiopeptide cluster(Lant_dehyd_C,YcaO) or cluster(Lant_dehyd_N,YcaO) 20 10 +phenazine phzB 20 10 +phosphonate phosphonates 20 20 +other (PP-binding & AMP-binding) or (PP-binding & A-OX) or (NAD_binding_4 & A-OX) or (NAD_binding_4 & AMP-binding) or LmbU or goadsporin_like or Neocarzinostat or cyanobactin_synth or cycdipepsynth or fom1 or bcpB or frbD or mitE or vlmB or prnB or CaiA or bacilysin or cypI 20 20 + +--> + + + </inputs> + <outputs> + <data format="fasta" name="geneclusterprots" label="${tool.name} on ${on_string} (Gen Cluster Proteins)" /> + <data format="tabular" name="zip" label="${tool.name} on ${on_string} (all files compressed)" /> + <data format="html" name="html" label="${tool.name} on ${on_string} (html report)" /> + <data name="embl" format="text" label="${tool.name} on ${on_string} EMBL Output Format"> + <filter>(wg_blast == True or pfam == True)</filter> + </data> + </outputs> + <help> + +.. class:: infomark + +That version of antiSMASH can only handle one sequence. So multi-sequence FASTA files are not supported. +For multiple sequences please use multi-antiSMASH. The advantage of that tool is that it will provide you with a +archive of all results created from antiSMASH (It can be large!) and a HTML output, for better inspection. + + +**What it does** + +antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. +It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier. + + +**Input** + +If you don't have an annotated GenBank or embl file you also can provide a glimmer prediction output. You can created it with glimmer or glimmerHMM. + + +**References** + +Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, +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. + +http://antismash.secondarymetabolites.org/help.html + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.txt Fri Oct 04 03:33:05 2013 -0400 @@ -0,0 +1,73 @@ +Galaxy wrapper for AntiSmash +===================================== + +This wrapper is copyright 2012 by Björn Grüning. + +This is a wrapper for the command line tool of antiSMASH. + +antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. +It integrates and cross-links with a large number of in silico secondary metabolite analysis tools. + +http://antismash.secondarymetabolites.org/ + +Marnix H. Medema, Kai Blin, Peter Cimermancic, Victor de Jager, Piotr Zakrzewski, Michael A. Fischbach, Tilmann Weber, Rainer Breitling & Eriko Takano (2011). +antiSMASH: Rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. Nucleic Acids Research 39: W339-W346. + + +Installation +============ + +Currently these wrapper is tested with version 1.1 and the modified version of antismash.py included in that repository. + +Install or downlaod antiSMASH from: + + +https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.x86_64.tar.bz2 + + +... and follow the instructions. +Please replace the antismash.py file with the one inlcuded in that repository. +Edit the following lines in multi_antiSMASH_wrapper.py and antiSMASH_wrapper.py and adopt it to your installation. + +blastdbpath = '/home/galaxy/bin/antismash-1.1.0/db' +pfamdbpath = '/home/galaxy/bin/antismash-1.1.0/db' +antismash_path = '/home/galaxy/bin/antismash-1.1.0/antismash.py' + + +To install the wrapper copy the antiSMASH folder in the galaxy tools +folder and modify the tools_conf.xml file to make the tool available to Galaxy. +For example: + +<section name="PKS-NRPS prediction" id="pks-nrps_prediction"> + <tool file="pks-nrps/tools/antiSMASH/antiSMASH.xml" /> + <tool file="pks-nrps/tools/antiSMASH/multi_antiSMASH.xml" /> +</section> + + +History +======= + +v0.1 - Initial public release + + +Wrapper Licence (MIT/BSD style) +=============================== + +Permission to use, copy, modify, and distribute this software and its +documentation with or without modifications and for any purpose and +without fee is hereby granted, provided that any copyright notices +appear in all copies and that both those copyright notices and this +permission notice appear in supporting documentation, and that the +names of the contributors or copyright holders not be used in +advertising or publicity pertaining to distribution of the software +without specific prior permission. + +THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL +WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE +CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT +OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS +OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE +OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE +OR PERFORMANCE OF THIS SOFTWARE. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Oct 04 03:33:05 2013 -0400 @@ -0,0 +1,65 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="blast+" version="2.2.28"> + <repository changeset_revision="d794cb2b0f45" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="hmmer " version="2.3.2"> + <repository changeset_revision="64510d86d77d" name="package_hmmer_2_3_2" owner="lionelguy" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="hmmer" version="3.0"> + <repository changeset_revision="3bc37773c609" name="package_hmmer_3_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="muscle" version="3.8.31"> + <repository changeset_revision="ce304c51f69b" name="package_muscle_3_8_31" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="antismash" version="2.0.2"> + <install version="1.0"> + <actions_group> + <!-- Download the binaries for MUSCLE compatible with 64-bit OSX. --> + <actions os="darwin"> + <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antiSMASH2.0.2_macosx.zip</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="chmod"> + <file mode="750">$INSTALL_DIR/run_antismash.py</file> + </action> + </actions> + <!-- Download the binaries for AntiSmash compatible with 64-bit Linux. --> + <actions architecture="x86_64" os="linux"> + <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.x86_64.tar.bz2</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="chmod"> + <file mode="750">$INSTALL_DIR/run_antismash.py</file> + </action> + </actions> + <!-- Download the binaries for AntiSmash compatible with 32-bit Linux. --> + <actions architecture="i386" os="linux"> + <action type="download_by_url">https://bitbucket.org/antismash/antismash2/downloads/antismash-2.0.2.i686.tar.bz2</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="chmod"> + <file mode="750">$INSTALL_DIR/run_antismash.py</file> + </action> + </actions> + <action type="setup_virtualenv">biopython=1.62 +helperlibs=0.1.2 +straight.plugin=1.4.0-post-1</action> + + <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. --> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> + </action> + </actions_group> + </install> + <readme> + AntiSmash installation with all dependencies. + </readme> + </package> +</tool_dependency>