# HG changeset patch # User kevyin # Date 1352260395 18000 # Node ID 19ca87a1ccee1506154b9db09e6931d849cf1493 # Parent 34d6428e4b96c838cc599e35b8987967d5065af7 Uploaded diff -r 34d6428e4b96 -r 19ca87a1ccee README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Tue Nov 06 22:53:15 2012 -0500 @@ -0,0 +1,30 @@ +Meme-chip wrapper for Galaxy + +========Installation instructions========: +First make sure meme is installed and accessible from the command line. +Meme-chip assumes the meme tools are in PATH. + +========Tool data table conf======== +Add the entry from the sample to tool_data_table_conf.xml + +========Tool loc file======== + +Example in tool-data/meme_chip_motifs.loc.sample +Entries come from the motif_db.csv in the motif database folder + +make sure: +- 3 cols +- tab delimited +- paths are correct + +There is a script to convert the csv to the loc format here: +https://bitbucket.org/gvl/meme-chip/src +After running delete the loc entries with multiple paths eg. All Vertebrates + + +LICENSE for this wrapper: +Kevin Ying +Garvan Institute http://www.garvan.org.au +GVL https://genome.edu.au/wiki/GVL + +http://opensource.org/licenses/mit-license.php diff -r 34d6428e4b96 -r 19ca87a1ccee meme_chip_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/meme_chip_wrapper.xml Tue Nov 06 22:53:15 2012 -0500 @@ -0,0 +1,188 @@ + + + meme-chip + + + echo "MEME version r4.9.0" + meme-chip $input_file -o ${memechip_out.files_path} + #for p in str.split($motif_dbs.fields.path,","): + -db $p + #end for + + #if str( $options_type.options_type_selector ) == 'advanced': + #if str( $options_type.bg_type.bg_type_selector) == 'bg_user': + -bfile "${ str( $options_type.bg_type.bfile ) }" + #end if + + #if str( $options_type.ccut ) != '-1': + -ccut "${ str( $options_type.ccut ) }" + #end if + + #if str( $options_type.time ) != '-1': + -time "${ str( $options_type.time ) }" + #end if + + -desc "${ str( $options_type.desc ) }" + + #if str( $options_type.meme_mod ) != '': + -meme-mod "${ str($options_type.meme_mod) }" + #end if + + #if str( $options_type.meme_minw ) != '-1': + -meme-minw "${ str($options_type.meme_minw) }" + #end if + + #if str( $options_type.meme_maxw ) != '-1': + -meme-maxw "${ str($options_type.meme_maxw) }" + #end if + + #if str( $options_type.meme_nmotifs ) != '-1': + -meme-nmotifs "${ str($options_type.meme_nmotifs) }" + #end if + + #if str( $options_type.meme_minsites ) != '-1': + -meme-minsites "${ str($options_type.meme_minsites) }" + #end if + + #if str( $options_type.meme_maxsites ) != '-1': + -meme-maxsites "${ str($options_type.meme_maxsites) }" + #end if + + #if $options_type.meme_pal: + -meme-pal "${ str($options_type.meme_pal) }" + #end if + + #if str( $options_type.dreme_e ) != '-1.0': + -dreme-e "${ str($options_type.dreme_e) }" + #end if + + #if str( $options_type.dreme_m ) != '-1': + -dreme-m "${ str($options_type.dreme_m) }" + #end if + + #if str($options_type.centrimo_score) != '-1.0': + -centrimo-score "${ str($options_type.centrimo_score) }" + #end if + + #if str( $options_type.centrimo_maxreg ) != '-1': + -centrimo-maxreg "${ str($options_type.centrimo_maxreg) }" + #end if + + #if str( $options_type.centrimo_ethresh ) != '-1.0': + -centrimo-ethresh "${ str($options_type.centrimo_ethresh) }" + #end if + + #if $options_type.centrimo_noseq: + -centrimo-noseq + #end if + + #end if + + 2>&1 || echo "Error running MEME." + + + && cd ${memechip_out.files_path} + && zip -rp memechip_out ./ + && mv memechip_out.zip ${memechip_out} + + + + + + + + + + + + value == True + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + .. class:: infomark + + After the job finishes, save the zip file, unzip and open "index.html" + + The actual meme-chip command is displayed under "Command line summary" + + Defaults: + http://meme.nbcr.net/meme/doc/meme-chip.html + + + diff -r 34d6428e4b96 -r 19ca87a1ccee tool-data/meme_chip_motifs.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/meme_chip_motifs.loc.sample Tue Nov 06 22:53:15 2012 -0500 @@ -0,0 +1,31 @@ +# value name path +JASPAR CORE JASPAR CORE /home/kevyin/bin/meme/db/motif_databases/JASPAR_CORE_2009.meme +JASPAR CORE vertebrates JASPAR CORE vertebrates /home/kevyin/bin/meme/db/motif_databases/JASPAR_CORE_2009_vertebrates.meme +JASPAR CORE fungi JASPAR CORE fungi /home/kevyin/bin/meme/db/motif_databases/JASPAR_CORE_2009_fungi.meme +JASPAR CORE insects JASPAR CORE insects /home/kevyin/bin/meme/db/motif_databases/JASPAR_CORE_2009_insects.meme +JASPAR CORE nematodes JASPAR CORE nematodes /home/kevyin/bin/meme/db/motif_databases/JASPAR_CORE_2009_nematodes.meme +JASPAR CORE plants JASPAR CORE plants /home/kevyin/bin/meme/db/motif_databases/JASPAR_CORE_2009_plants.meme +JASPAR CORE urochordates JASPAR CORE urochordates /home/kevyin/bin/meme/db/motif_databases/JASPAR_CORE_2009_urochordates.meme +JASPAR PHYLOFACTS JASPAR PHYLOFACTS /home/kevyin/bin/meme/db/motif_databases/JASPAR_PHYLOFACTS_2008.meme +JASPAR FAM JASPAR FAM /home/kevyin/bin/meme/db/motif_databases/JASPAR_FAM_2008.meme +JASPAR POLII JASPAR POLII /home/kevyin/bin/meme/db/motif_databases/JASPAR_POLII_2008.meme +JASPAR CNE JASPAR CNE /home/kevyin/bin/meme/db/motif_databases/JASPAR_CNE_2008.meme +JASPAR SPLICE JASPAR SPLICE /home/kevyin/bin/meme/db/motif_databases/JASPAR_SPLICE_2008.meme +UniPROBE/BEEML-PBM (Zhao and Stormo 2011) UniPROBE/BEEML-PBM (Zhao and Stormo 2011) /home/kevyin/bin/meme/db/motif_databases/zhao2011.meme +Human and Mouse (Jolma2010) Human and Mouse (Jolma2010) /home/kevyin/bin/meme/db/motif_databases/jolma2010.meme +Human and Mouse (MacIsaac THEME) Human and Mouse (MacIsaac THEME) /home/kevyin/bin/meme/db/motif_databases/macisaac_theme.v1.meme +Prokaryotes (Prodoric Release 8.9) Prokaryotes (Prodoric Release 8.9) /home/kevyin/bin/meme/db/motif_databases/prodoric.meme +Prokaryotes (RegTransBase v4) Prokaryotes (RegTransBase v4) /home/kevyin/bin/meme/db/motif_databases/regtransbase.meme +Drosophila (FLYREG; Bergman & Pollard v2) Drosophila (FLYREG; Bergman & Pollard v2) /home/kevyin/bin/meme/db/motif_databases/flyreg.v2.meme +Drosophila (DMMPMM; Kulakovskiy et al. 2009) Drosophila (DMMPMM; Kulakovskiy et al. 2009) /home/kevyin/bin/meme/db/motif_databases/dmmpmm2009.meme +Drosophila (iDMMPMM; Kulakovskiy et al. 2009) Drosophila (iDMMPMM; Kulakovskiy et al. 2009) /home/kevyin/bin/meme/db/motif_databases/idmmpmm2009.meme +Homeodomains (Berger et al.) Homeodomains (Berger et al.) /home/kevyin/bin/meme/db/motif_databases/homeodomain.meme +Mouse (UniPROBE) Mouse (UniPROBE) /home/kevyin/bin/meme/db/motif_databases/uniprobe_mouse.meme +Mouse (Chen2008) Mouse (Chen2008) /home/kevyin/bin/meme/db/motif_databases/chen2008.meme +ETS factors (Wei et al. 2010) ETS factors (Wei et al. 2010) /home/kevyin/bin/meme/db/motif_databases/wei2010*.meme +E. coli (DPINTERACT) E. coli (DPINTERACT) /home/kevyin/bin/meme/db/motif_databases/dpinteract.meme +GLIs and TCF7L2/TCF4 (Hallikas et al. 2006) GLIs and TCF7L2/TCF4 (Hallikas et al. 2006) /home/kevyin/bin/meme/db/motif_databases/hallikas2006.meme +Worm (UniPROBE) Worm (UniPROBE) /home/kevyin/bin/meme/db/motif_databases/uniprobe_worm.meme +Malaria (Campbell et al. 2010) Malaria (Campbell et al. 2010) /home/kevyin/bin/meme/db/motif_databases/campbell2010_malaria_pbm.meme +Yeast (MacIsaac v1) Yeast (MacIsaac v1) /home/kevyin/bin/meme/db/motif_databases/macisaac_yeast.v1.meme +Yeast (SCPD) Yeast (SCPD) /home/kevyin/bin/meme/db/motif_databases/scpd_matrix.meme diff -r 34d6428e4b96 -r 19ca87a1ccee tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Nov 06 22:53:15 2012 -0500 @@ -0,0 +1,6 @@ + + + value, name, path + +
+