Mercurial > repos > kevyin > meme_chip

changeset 17:5bb9eb050e57 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Deleted selected files
author kevyin
date Thu, 22 Nov 2012 20:27:11 -0500
parents c3e0e0a0ae09
children 2948554ae3d7
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, 0 insertions(+), 286 deletions(-) [+]
line wrap: on
line diff
--- a/README	Mon Nov 12 19:34:55 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-Meme-chip wrapper for Galaxy
-
-=========================================:
-========Installation instructions========:
-=========================================:
-The tool_dependencies.xml can attempt to install meme in a folder specific for this tool.
-(such as bwa_wrappers)
-
-The procedure does NOT download motif databases you will need to download them yourself
-
-Meme-chip assumes the meme tools are in PATH.
-Make sure meme is accessible
-
-
-========Tool data table conf========
-Check the meme_chip_motifs 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
--- a/meme_chip_wrapper.xml	Mon Nov 12 19:34:55 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="1.2.3">
-    <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&gt;&amp;1 || echo "Error running MEME."
-        <!--&amp;&amp; mv ${html_outfile.files_path}/index.html ${html_outfile}-->
-        <!--&amp;&amp; zip -r result $html_outfile.files_path-->
-        &amp;&amp; cd ${memechip_out.files_path} 
-        &amp;&amp; zip -rp memechip_out ./
-        &amp;&amp; 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="&apos;"/>
-                      </valid>
-                      <mapping initial="none">
-                        <add source="&apos;" 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	Mon Nov 12 19:34:55 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	Mon Nov 12 19:34:55 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>
-
--- a/tool_dependencies.xml	Mon Nov 12 19:34:55 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-  <package name="meme" version="4.9.0">
-    <install version="1.0">
-      <actions>
-        <action type="download_by_url">ftp://ftp.ebi.edu.au/pub/software/MEME/r4.9.0/rc5/meme_4.9.0.tar.gz</action>
-        <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
-        <action type="shell_command">make</action>
-        <action type="shell_command">make install</action>
-        <action type="set_environment">
-          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-        </action>
-      </actions>
-    </install>
-    <readme>
-      Skeleton file for meme install. Does not actually install meme.
-    </readme>
-  </package>
-</tool_dependency>