Mercurial > repos > kevyin > meme_chip
changeset 11:dd79316654f6 draft
Uploaded
| author | kevyin |
|---|---|
| date | Wed, 07 Nov 2012 23:55:31 -0500 |
| parents | c257eb0d4af0 |
| children | 54c09305fa50 |
| files | README meme_chip_wrapper.xml tool-data/meme_chip_motifs.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 5 files changed, 273 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Wed Nov 07 23:55:31 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======== +Check the entry is in 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/meme_chip_wrapper.xml Wed Nov 07 23:55:31 2012 -0500 @@ -0,0 +1,188 @@ +<tool id="meme_chip_wrapper" name="meme-chip" version="1.2.0"> + <requirements> + <requirement type="package" version="4.9.0">meme</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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/meme_chip_motifs.loc.sample Wed Nov 07 23:55:31 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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Wed Nov 07 23:55:31 2012 -0500 @@ -0,0 +1,8 @@ +<!-- 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> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Nov 07 23:55:31 2012 -0500 @@ -0,0 +1,16 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="meme" version="4.9.0"> + <install version="0.1"> + <actions> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> + Skeleton file for meme install. Does not actually install meme. + </readme> + </package> +</tool_dependency> +