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Changeset 9:1d6b3be059c8 (2016-02-08)

Previous changeset 8:f2153ec1ccfd (2016-02-05)

Commit message:
Name change. Removed redundant tool def.

modified:
interproscan5/ips5.xml

removed:
interproscan5/interproscan.xml

diff -r f2153ec1ccfd -r 1d6b3be059c8 interproscan5/interproscan.xml
--- a/interproscan5/interproscan.xml Fri Feb 05 13:18:41 2016 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000

[

b'@@ -1,285 +0,0 @@\n-<tool id="interproscan" name="Interproscan functional predictions of ORFs" version="5.0.0a">\n- <description>Interproscan functional predictions of ORFs</description>\n- <requirements>\n- \n- <requirement type="set_environment">INTERPROSCAN_SCRIPT_PATH</requirement>\n- </requirements>\n-\n- <command>\n- #import os\n- \\$IPS_HOME/interproscan.sh\n- ## disables the precalculated lookup service, all calculation will be run locally\n- -dp \n- --input $infile \n- --seqtype $seqtype \n- -f $oformat \n- --applications $appl \n- --tempdir \\$TEMP\n-\n- $pathways\n- $goterms\n- $iprlookup\n- $mode\n-\n- #if str($oformat) in [\'SVG\', \'HTML\']:\n- --output-file-base $outfile\n- 2>&1;\n- mkdir -p $outfile.files_path;\n- #set temp_archive_file = str($outfile) + \'.\' + str($oformat).lower() + \'.tar.gz\'\n- tar -C $outfile.files_path -xvmzf $temp_archive_file;\n- python \\$INTERPROSCAN_SCRIPT_PATH/create_index.py $outfile $outfile.files_path;\n- rm $temp_archive_file\n- #else:\n- -o $outfile\n- 2>&1\n- #end if\n- </command>\n-\n- <inputs>\n- <param name="infile" type="data" format="fasta" label="Protein Fasta File"/>\n-\n- <param name="seqtype" type="select" label="Type of the input sequences" help="">\n- <option value="p" selected="true">Protein</option>\n- <option value="n">DNA / RNA</option>\n- </param>\n-\n- <param name="mode" type="boolean" label="Run on cluster?" help="Check to submit job to cluster."\n- truevalue="--mode=cluster --clusterrunid=gtdi-ips-analysis"\n- falsevalue=""/>\n-\n- <param name="appl" type="select" multiple="True" display="checkboxes" label="Applications to run"\n- help="Select your programm.">\n- <option value="TIGRFAM"\n- selected="true">TIGRFAM: protein families based on Hidden Markov Models or HMMs</option>\n- <option value="PIRSF" selected="true">PIRSF: non-overlapping clustering of UniProtKB sequences into a hierarchical order (evolutionary relationships)</option>\n- <option value="ProDom"\n- selected="true">ProDom: set of protein domain families generated from the UniProtKB</option>\n- <option value="Panther"\n- selected="true">Panther: Protein ANalysis THrough Evolutionary Relationships</option>\n- <option value="SMART" selected="true">SMART: identification and analysis of domain architectures based on Hidden Markov Models or HMMs</option>\n- <option value="PrositeProfiles" selected="true">PROSITE Profiles: protein domains, families and functional sites as well as associated profiles to identify them</option>\n- <option value="PrositePatterns" selected="true">PROSITE Pattern: protein domains, families and functional sites as well as associated patterns to identify them</option>\n- <option value="HAMAP"\n- selected="true">HAMAP: High-quality Automated Annotation of Microbial Proteomes</option>\n- <option value="PfamA" selected="true">PfamA: protein families, each represented by multiple sequence alignments and hidden Markov models</option>\n- <option value="PRINTS" selected="true">PRINTS: group of conserved motifs (fingerprints) used to characterise a protein family</option>\n- <option value="SuperFamily"\n- selected="true">SUPERFAMILY: database of structural and functional annotation</option>\n- <option value="Coi'..b'of all the columns and attributes used on [http://www.sequenceontology.org/gff3.shtml].\n-\n-Example Output\n---------------\n-\n-::\n-\n- ##gff-version 3\n- ##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/sofa.obo?revision=1.269\n- ##sequence-region AACH01000027 1 1347\n- ##seqid|source|type|start|end|score|strand|phase|attributes\n- AACH01000027 provided_by_user nucleic_acid 1 1347 . + . Name=AACH01000027;md5=b2a7416cb92565c004becb7510f46840;ID=AACH01000027\n- AACH01000027 getorf ORF 1 1347 . + . Name=AACH01000027.2_21;Target=pep_AACH01000027_1_1347 1 449;md5=b2a7416cb92565c004becb7510f46840;ID=orf_AACH01000027_1_1347\n- AACH01000027 getorf polypeptide 1 449 . + . md5=fd0743a673ac69fb6e5c67a48f264dd5;ID=pep_AACH01000027_1_1347\n- AACH01000027 Pfam protein_match 84 314 1.2E-45 + . Name=PF00696;signature_desc=Amino acid kinase family;Target=null 84 314;status=T;ID=match$8_84_314;Ontology_term="GO:0008652";date=15-04-2013;Dbxref="InterPro:IPR001048","Reactome:REACT_13"\n- ##sequence-region 2\n- ...\n- >pep_AACH01000027_1_1347\n- LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEV\n- LQKGDGNAHSKKDTEIRRREMKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEA\n- GHELILVSSGAIAAGFGALGFKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQI\n- LLTQDDFVDKRRYKNAHQALSVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQ\n- ADLLVFLTDVDGLYTGNPNSDPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAA\n- TIATESGVPVYICSSLKSDSMIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWV\n- DKGAAEALSQYGKSLLLSGIVEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDML\n- RSQKAKGVLIYRDDWISITPEIQLLFTEF\n- ...\n- >match$8_84_314\n- KRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALGFKK\n- RPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQALSVL\n- LNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNSDPR\n- AKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICS\n- \n-\n-Scalable Vector Graphics (SVG) and HyperText Markup Language (HTML)\n-====================================================================\n-\n-InterProScan_ 5 outputs a single HTML/SVG file for each protein sequence analysed. \n-\n-\n-Example Output\n---------------\n-\n-.. image:: $PATH_TO_IMAGES/P51587.svg.png\n-\n-.. _InterProScan: http://www.ebi.ac.uk/interpro\n-\n-\n-----------\n-References\n-----------\n-\n-\n-If you use this Galaxy tool in work leading to a scientific publication please\n-cite the following papers:\n-\n-Peter J.A. Cock, Bj\xc3\xb6rn A. Gr\xc3\xbcning, Konrad Paszkiewicz and Leighton Pritchard (2013).\n-Galaxy tools and workflows for sequence analysis with applications\n-in molecular plant pathology. PeerJ 1:e167\n-http://dx.doi.org/10.7717/peerj.167\n-\n-Zdobnov EM, Apweiler R (2001)\n-InterProScan an integration platform for the signature-recognition methods in InterPro.\n-Bioinformatics 17, 847-848.\n-http://dx.doi.org/10.1093/bioinformatics/17.9.847\n-\n-Quevillon E, Silventoinen V, Pillai S, Harte N, Mulder N, Apweiler R, Lopez R (2005)\n-InterProScan: protein domains identifier.\n-Nucleic Acids Research 33 (Web Server issue), W116-W120.\n-http://dx.doi.org/10.1093/nar/gki442\n-\n-Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C. (2009)\n-InterPro: the integrative protein signature database.\n-Nucleic Acids Research 37 (Database Issue), D224-228.\n-http://dx.doi.org/10.1093/nar/gkn785\n-\n-\n-This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at\n-http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5\n-\n-\n-**Galaxy Wrapper Author**::\n-\n- * Bjoern Gruening, University of Freiburg\n- * Konrad Paszkiewicz, University of Exeter\n-\n- </help>\n-</tool>\n'

diff -r f2153ec1ccfd -r 1d6b3be059c8 interproscan5/ips5.xml
--- a/interproscan5/ips5.xml Fri Feb 05 13:18:41 2016 -0500
+++ b/interproscan5/ips5.xml Mon Feb 08 12:10:24 2016 -0500

@@ -1,4 +1,4 @@
-<tool id="ips5" name="Interproscan functional predictions of ORFs" version="5.0.2mkh">
+<tool id="ips5" name="Interproscan" version="5.0.2mkh">
     <description>Interproscan functional predictions of ORFs.</description>
     <requirements>
         <!--