Mercurial > repos > kevyin > meme_chip
changeset 8:af3f283f0219 draft
Deleted selected files
| author | kevyin |
|---|---|
| date | Wed, 07 Nov 2012 01:24:09 -0500 |
| parents | 8d63a5aa8944 |
| children | 1e428d8defbc |
| files | README meme_chip_wrapper.xml tool-data/meme_chip_motifs.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 4 files changed, 0 insertions(+), 257 deletions(-) [+] |
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--- a/README Wed Nov 07 01:12:40 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
--- a/meme_chip_wrapper.xml Wed Nov 07 01:12:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,188 +0,0 @@ -<tool id="meme_chip_wrapper" name="meme-chip" version="1.0.0"> - <requirements> - <requirement type="package" version="4.9.0">meme-chip</requirement> - </requirements> - <description></description> - <version_command>echo "MEME version r4.9.0"</version_command> - <command> 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 - <!--pipe stderr to stdout because of annoying log4perl warnings. Error when exit status--> - 2>&1 || echo "Error running MEME." - <!--&& mv ${html_outfile.files_path}/index.html ${html_outfile}--> - <!--&& zip -r result $html_outfile.files_path--> - && cd ${memechip_out.files_path} - && zip -rp memechip_out ./ - && mv memechip_out.zip ${memechip_out} - </command> - <inputs> - <param format="fasta" name="input_file" type="data" label="Sequences in fasta format" /> - <param name="motif_dbs" label="MEME Motif databases" type="select" multiple="true" display="checkboxes" help="Use CTRL to select multiple databases"> - <options from_data_table="meme_chip_motifs"> - <filter type="sort_by" column="1"/> - <validator type="no_options" message="No indexes are available for the selected dataset"/> - </options> - - </param> - <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="True"> - <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> - </param> - <conditional name="options_type"> - <param name="options_type_selector" type="select" label="Options Configuration"> - <option value="basic" selected="true">Basic</option> - <option value="advanced">Advanced</option> - </param> - <when value="basic"> - <!-- do nothing here --> - </when> - <when value="advanced"> - <!--bfile--> - <conditional name="bg_type"> - <param name="bg_type_selector" type="select" label="Custom background"> - <option value="bg_default" selected="True">Default Background</option> - <option value="bg_user">Background in your History</option> - </param> - <when value="bg_default"> - <!--do nothing here--> - </when> - <when value="bg_user"> - <param name="bfile" type="data" label="-bfile: Background File" /> - </when> - </conditional> - <!--ccut--> - <param name="ccut" type="integer" value="-1" label="-ccut: Max size of a seq before it is cut down; 0: do not cut; -1: Default behaviour" /> - <!--tine--> - <param name="time" type="integer" value="-1" label="-time: Maximum time (minutes) that this program has to run and create output in; -1: no limit" /> - <!--desc--> - <param name="desc" type="text" value="Galaxy MEME-Chip" label="-desc: Description of the analysis" > - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - </valid> - <mapping initial="none"> - <add source="'" target=""/> - </mapping> - </sanitizer> - </param> - <!--MEME options--> - <param name="meme_mod" type="select" label="-meme-mod: Sites used in a single sequence" > - <option value="" selected="True"/> - <option value="oops" /> - <option value="zoops" /> - <option value="anr" /> - </param> - <param name="meme_minw" type="integer" value="-1" label="-meme-minw: minimum motif width; -1: Default behaviour" /> - <param name="meme_maxw" type="integer" value="-1" label="-meme-maxw: maximum motif width; -1: Default behaviour" /> - <param name="meme_nmotifs" type="integer" value="-1" label="-meme-nmotifs: maximum number of motifs to find; -1: Default behaviour" /> - <param name="meme_minsites" type="integer" value="-1" label="-meme-minsites: minimum number of sites per motif; -1: Default behaviour" /> - <param name="meme_maxsites" type="integer" value="-1" label="-meme-maxsites: maximum number of sites per motif; -1: Default behaviour" /> - <param name="meme_pal" type="boolean" label="-meme-pal: look for palindromes only" /> - <!--DREME options--> - <param name="dreme_e" type="float" value="-1" label="-dreme-e: stop searching after reaching this E-value threshold; -1: Default behaviour" /> - <param name="dreme_m" type="integer" value="-1" label="-dreme-e: stop searching after finding this many motifs; -1: Default behaviour" /> - <!--CentriMo options--> - <param name="centrimo_score" type="float" value="-1" label="-centrimo-score: set the minimum allowed match score; -1: Default behaviour" /> - <param name="centrimo_maxreg" type="integer" value="-1" label="-centrimo-maxreg: set the maximum region size to be considered; -1: Default behaviour" /> - <param name="centrimo_ethresh" type="float" value="-1" label="-centrimo-ethresh: set the E-value threshold for reporting; -1: Default behaviour" /> - <param name="centrimo_noseq" type="boolean" label="-centrimo-noseq: don't store sequence IDs in the output" /> - - </when> - </conditional> - </inputs> - <outputs> - <!--<data format="html" name="html_outfile" label="index" />--> - <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />--> - <data format="zip" name="memechip_out" label="SAVE ME ${tool.name} on #echo os.path.splitext(str($input_file.name))[0]#.zip" /> - </outputs> - - - <tests> - <test> - <param name="input_file" value="extract_genomic_dna.fa" /> - <output name="html_file" file="sample_output.html" ftype="html" /> - </test> - </tests> - - <help> - - .. 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 - - </help> -</tool>
--- a/tool-data/meme_chip_motifs.loc.sample Wed Nov 07 01:12:40 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
--- a/tool_data_table_conf.xml.sample Wed Nov 07 01:12:40 2012 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -<!-- Location of meme-chip files --> -<tables> - <table name="meme_chip_motifs" comment_char="#"> - <columns>value, name, path</columns> - <file path="tool-data/meme_chip_motifs.loc" /> - </table> -</tables> -