# HG changeset patch # User kevyin # Date 1352260890 18000 # Node ID aacb149c4982be2e1b01ecf1e7600d9b3367a1f5 # Parent 195653b0ebefa2625adf53947a949373935a0a87 Deleted selected files diff -r 195653b0ebef -r aacb149c4982 README --- a/README Tue Nov 06 23:01:17 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -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 195653b0ebef -r aacb149c4982 meme_chip_wrapper.xml --- a/meme_chip_wrapper.xml Tue Nov 06 23:01:17 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,188 +0,0 @@ - - - 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 195653b0ebef -r aacb149c4982 tool-data/meme_chip_motifs.loc.sample --- a/tool-data/meme_chip_motifs.loc.sample Tue Nov 06 23:01:17 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ -# 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 195653b0ebef -r aacb149c4982 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Tue Nov 06 23:01:17 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ - - - value, name, path - -
-