3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ba001f4c0326/ Changeset: ba001f4c0326 Branch: stable User: davebgx Date: 2014-02-19 21:23:45 Summary: Situations where a migration warning would be incorrectly displayed, and tools with matching filenames would be removed from the tool_conf.xml after running a migration script. Affected #: 9 files diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -186,8 +186,7 @@ # Tools outside of sections. file_path = elem.get( 'file', None ) if file_path: - file_name = suc.strip_path( file_path ) - if file_name in tool_configs_to_filter: + if file_path in tool_configs_to_filter: root.remove( elem ) persist_required = True elif elem.tag == 'section': @@ -196,8 +195,7 @@ if section_elem.tag == 'tool': file_path = section_elem.get( 'file', None ) if file_path: - file_name = suc.strip_path( file_path ) - if file_name in tool_configs_to_filter or file_path in tool_configs_to_filter: + if file_path in tool_configs_to_filter: elem.remove( section_elem ) persist_required = True if persist_required: @@ -221,8 +219,7 @@ if proprietary_tool_panel_elem.tag == 'tool': # The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = proprietary_tool_panel_elem.get( 'file' ) - proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name or tool_config == proprietary_tool_config: + if tool_config == proprietary_tool_config: # The tool is loaded outside of any sections. tool_sections.append( None ) if not is_displayed: @@ -233,8 +230,7 @@ if section_elem.tag == 'tool': # The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = section_elem.get( 'file' ) - proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name or tool_config == proprietary_tool_config: + if tool_config == proprietary_tool_config: # The tool is loaded inside of the section_elem. tool_sections.append( ToolSection( proprietary_tool_panel_elem ) ) if not is_displayed: @@ -312,8 +308,7 @@ # Tools outside of sections. file_path = elem.get( 'file', None ) if file_path: - name = suc.strip_path( file_path ) - if name in migrated_tool_configs or file_path in migrated_tool_configs: + if file_path in migrated_tool_configs: if elem not in tool_panel_elems: tool_panel_elems.append( elem ) elif elem.tag == 'section': @@ -322,8 +317,7 @@ if section_elem.tag == 'tool': file_path = section_elem.get( 'file', None ) if file_path: - name = suc.strip_path( file_path ) - if name in migrated_tool_configs or file_path in migrated_tool_configs: + if file_path in migrated_tool_configs: # Append the section, not the tool. if elem not in tool_panel_elems: tool_panel_elems.append( elem ) @@ -361,10 +355,8 @@ for tool_panel_dict in v: # Keep track of tool config file names associated with entries that have been made to the # migrated_tools_conf.xml file so they can be eliminated from all non-shed-related tool panel configs. - tool_config_file = tool_panel_dict.get( 'tool_config', None ) - if tool_config_file: - if tool_config_file not in tool_configs_to_filter: - tool_configs_to_filter.append( tool_config_file ) + if tool_config not in tool_configs_to_filter: + tool_configs_to_filter.append( tool_config ) else: print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' \ % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) ) diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0002_tools.xml --- a/scripts/migrate_tools/0002_tools.xml +++ b/scripts/migrate_tools/0002_tools.xml @@ -2,112 +2,112 @@ <toolshed name="toolshed.g2.bx.psu.edu"><repository name="emboss_datatypes" description="Datatypes for Emboss tools" changeset_revision="a89163f31369" /><repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5.0.0 tools" changeset_revision="7334f6d0ac17"> - <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> - <tool id="EMBOSS: backtranseq2" version="5.0.0" file="emboss_backtranseq.xml" /> - <tool id="EMBOSS: banana3" version="5.0.0" file="emboss_banana.xml" /> - <tool id="EMBOSS: biosed4" version="5.0.0" file="emboss_biosed.xml" /> - <tool id="EMBOSS: btwisted5" version="5.0.0" file="emboss_btwisted.xml" /> - <tool id="EMBOSS: cai_custom6" version="5.0.0" file="emboss_cai_custom.xml" /> - <tool id="EMBOSS: cai6" version="5.0.0" file="emboss_cai.xml" /> - <tool id="EMBOSS: chaos7" version="5.0.0" file="emboss_chaos.xml" /> - <tool id="EMBOSS: charge8" version="5.0.0" file="emboss_charge.xml" /> - <tool id="EMBOSS: checktrans9" version="5.0.0" file="emboss_checktrans.xml" /> - <tool id="EMBOSS: chips10" version="5.0.0" file="emboss_chips.xml" /> - <tool id="EMBOSS: cirdna11" version="5.0.0" file="emboss_cirdna.xml" /> - <tool id="EMBOSS: codcmp12" version="5.0.0" file="emboss_codcmp.xml" /> - <tool id="EMBOSS: coderet13" version="5.0.0" file="emboss_coderet.xml" /> - <tool id="EMBOSS: compseq14" version="5.0.0" file="emboss_compseq.xml" /> - <tool id="EMBOSS: cpgplot15" version="5.0.0" file="emboss_cpgplot.xml" /> - <tool id="EMBOSS: cpgreport16" version="5.0.0" file="emboss_cpgreport.xml" /> - <tool id="EMBOSS: cusp17" version="5.0.0" file="emboss_cusp.xml" /> - <tool id="EMBOSS: cutseq18" version="5.0.0" file="emboss_cutseq.xml" /> - <tool id="EMBOSS: dan19" version="5.0.0" file="emboss_dan.xml" /> - <tool id="EMBOSS: degapseq20" version="5.0.0" file="emboss_degapseq.xml" /> - <tool id="EMBOSS: descseq21" version="5.0.0" file="emboss_descseq.xml" /> - <tool id="EMBOSS: diffseq22" version="5.0.0" file="emboss_diffseq.xml" /> - <tool id="EMBOSS: digest23" version="5.0.0" file="emboss_digest.xml" /> - <tool id="EMBOSS: dotmatcher24" version="5.0.0" file="emboss_dotmatcher.xml" /> - <tool id="EMBOSS: dotpath25" version="5.0.0" file="emboss_dotpath.xml" /> - <tool id="EMBOSS: dottup26" version="5.0.0" file="emboss_dottup.xml" /> - <tool id="EMBOSS: dreg27" version="5.0.0" file="emboss_dreg.xml" /> - <tool id="EMBOSS: einverted28" version="5.0.0" file="emboss_einverted.xml" /> - <tool id="EMBOSS: epestfind29" version="5.0.0" file="emboss_epestfind.xml" /> - <tool id="EMBOSS: equicktandem31" version="5.0.0" file="emboss_equicktandem.xml" /> - <tool id="EMBOSS: est2genome32" version="5.0.0" file="emboss_est2genome.xml" /> - <tool id="EMBOSS: etandem33" version="5.0.0" file="emboss_etandem.xml" /> - <tool id="EMBOSS: extractfeat34" version="5.0.0" file="emboss_extractfeat.xml" /> - <tool id="EMBOSS: extractseq35" version="5.0.0" file="emboss_extractseq.xml" /> - <tool id="EMBOSS: freak36" version="5.0.0" file="emboss_freak.xml" /> - <tool id="EMBOSS: fuzznuc37" version="5.0.0" file="emboss_fuzznuc.xml" /> - <tool id="EMBOSS: fuzzpro38" version="5.0.0" file="emboss_fuzzpro.xml" /> - <tool id="EMBOSS: fuzztran39" version="5.0.0" file="emboss_fuzztran.xml" /> - <tool id="EMBOSS: garnier40" version="5.0.0" file="emboss_garnier.xml" /> - <tool id="EMBOSS: geecee41" version="5.0.0" file="emboss_geecee.xml" /> - <tool id="EMBOSS: getorf42" version="5.0.0" file="emboss_getorf.xml" /> - <tool id="EMBOSS: helixturnhelix43" version="5.0.0" file="emboss_helixturnhelix.xml" /> - <tool id="EMBOSS: hmoment44" version="5.0.0" file="emboss_hmoment.xml" /> - <tool id="EMBOSS: iep45" version="5.0.0" file="emboss_iep.xml" /> - <tool id="EMBOSS: infoseq46" version="5.0.0" file="emboss_infoseq.xml" /> - <tool id="EMBOSS: isochore47" version="5.0.0" file="emboss_isochore.xml" /> - <tool id="EMBOSS: lindna48" version="5.0.0" file="emboss_lindna.xml" /> - <tool id="EMBOSS: marscan49" version="5.0.0" file="emboss_marscan.xml" /> - <tool id="EMBOSS: maskfeat50" version="5.0.0" file="emboss_maskfeat.xml" /> - <tool id="EMBOSS: maskseq51" version="5.0.0" file="emboss_maskseq.xml" /> - <tool id="EMBOSS: matcher52" version="5.0.0" file="emboss_matcher.xml" /> - <tool id="EMBOSS: megamerger53" version="5.0.0" file="emboss_megamerger.xml" /> - <tool id="EMBOSS: merger54" version="5.0.0" file="emboss_merger.xml" /> - <tool id="EMBOSS: msbar55" version="5.0.0" file="emboss_msbar.xml" /> - <tool id="EMBOSS: needle56" version="5.0.0" file="emboss_needle.xml" /> - <tool id="EMBOSS: newcpgreport57" version="5.0.0" file="emboss_newcpgreport.xml" /> - <tool id="EMBOSS: newcpgseek58" version="5.0.0" file="emboss_newcpgseek.xml" /> - <tool id="EMBOSS: newseq59" version="5.0.0" file="emboss_newseq.xml" /> - <tool id="EMBOSS: noreturn60" version="5.0.0" file="emboss_noreturn.xml" /> - <tool id="EMBOSS: notseq61" version="5.0.0" file="emboss_notseq.xml" /> - <tool id="EMBOSS: nthseq62" version="5.0.0" file="emboss_nthseq.xml" /> - <tool id="EMBOSS: octanol63" version="5.0.0" file="emboss_octanol.xml" /> - <tool id="EMBOSS: oddcomp64" version="5.0.0" file="emboss_oddcomp.xml" /> - <tool id="EMBOSS: palindrome65" version="5.0.0" file="emboss_palindrome.xml" /> - <tool id="EMBOSS: pasteseq66" version="5.0.0" file="emboss_pasteseq.xml" /> - <tool id="EMBOSS: patmatdb67" version="5.0.0" file="emboss_patmatdb.xml" /> - <tool id="EMBOSS: pepcoil68" version="5.0.0" file="emboss_pepcoil.xml" /> - <tool id="EMBOSS: pepinfo69" version="5.0.0" file="emboss_pepinfo.xml" /> - <tool id="EMBOSS: pepnet70" version="5.0.0" file="emboss_pepnet.xml" /> - <tool id="EMBOSS: pepstats71" version="5.0.0" file="emboss_pepstats.xml" /> - <tool id="EMBOSS: pepwheel72" version="5.0.0" file="emboss_pepwheel.xml" /> - <tool id="EMBOSS: pepwindow73" version="5.0.0" file="emboss_pepwindow.xml" /> - <tool id="EMBOSS: pepwindowall74" version="5.0.0" file="emboss_pepwindowall.xml" /> - <tool id="EMBOSS: plotcon75" version="5.0.0" file="emboss_plotcon.xml" /> - <tool id="EMBOSS: plotorf76" version="5.0.0" file="emboss_plotorf.xml" /> - <tool id="EMBOSS: polydot77" version="5.0.0" file="emboss_polydot.xml" /> - <tool id="EMBOSS: preg78" version="5.0.0" file="emboss_preg.xml" /> - <tool id="EMBOSS: prettyplot79" version="5.0.0" file="emboss_prettyplot.xml" /> - <tool id="EMBOSS: prettyseq80" version="5.0.0" file="emboss_prettyseq.xml" /> - <tool id="EMBOSS: primersearch81" version="5.0.0" file="emboss_primersearch.xml" /> - <tool id="EMBOSS: revseq82" version="5.0.0" file="emboss_revseq.xml" /> - <tool id="EMBOSS: seqmatchall83" version="5.0.0" file="emboss_seqmatchall.xml" /> - <tool id="EMBOSS: seqret84" version="5.0.0" file="emboss_seqret.xml" /> - <tool id="EMBOSS: showfeat85" version="5.0.0" file="emboss_showfeat.xml" /> - <tool id="EMBOSS: shuffleseq87" version="5.0.0" file="emboss_shuffleseq.xml" /> - <tool id="EMBOSS: sigcleave88" version="5.0.0" file="emboss_sigcleave.xml" /> - <tool id="EMBOSS: sirna89" version="5.0.0" file="emboss_sirna.xml" /> - <tool id="EMBOSS: sixpack90" version="5.0.0" file="emboss_sixpack.xml" /> - <tool id="EMBOSS: skipseq91" version="5.0.0" file="emboss_skipseq.xml" /> - <tool id="EMBOSS: splitter92" version="5.0.0" file="emboss_splitter.xml" /> - <tool id="EMBOSS: supermatcher95" version="5.0.0" file="emboss_supermatcher.xml" /> - <tool id="EMBOSS: syco96" version="5.0.0" file="emboss_syco.xml" /> - <tool id="EMBOSS: tcode97" version="5.0.0" file="emboss_tcode.xml" /> - <tool id="EMBOSS: textsearch98" version="5.0.0" file="emboss_textsearch.xml" /> - <tool id="EMBOSS: tmap99" version="5.0.0" file="emboss_tmap.xml" /> - <tool id="EMBOSS: tranalign100" version="5.0.0" file="emboss_tranalign.xml" /> - <tool id="EMBOSS: transeq101" version="5.0.0" file="emboss_transeq.xml" /> - <tool id="EMBOSS: trimest102" version="5.0.0" file="emboss_trimest.xml" /> - <tool id="EMBOSS: trimseq103" version="5.0.0" file="emboss_trimseq.xml" /> - <tool id="EMBOSS: twofeat104" version="5.0.0" file="emboss_twofeat.xml" /> - <tool id="EMBOSS: union105" version="5.0.0" file="emboss_union.xml" /> - <tool id="EMBOSS: vectorstrip106" version="5.0.0" file="emboss_vectorstrip.xml" /> - <tool id="EMBOSS: water107" version="5.0.0" file="emboss_water.xml" /> - <tool id="EMBOSS: wobble108" version="5.0.0" file="emboss_wobble.xml" /> - <tool id="EMBOSS: wordcount109" version="5.0.0" file="emboss_wordcount.xml" /> - <tool id="EMBOSS: wordmatch110" version="5.0.0" file="emboss_wordmatch.xml" /> + <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_5/emboss_antigenic.xml" /> + <tool id="EMBOSS: backtranseq2" version="5.0.0" file="emboss_5/emboss_backtranseq.xml" /> + <tool id="EMBOSS: banana3" version="5.0.0" file="emboss_5/emboss_banana.xml" /> + <tool id="EMBOSS: biosed4" version="5.0.0" file="emboss_5/emboss_biosed.xml" /> + <tool id="EMBOSS: btwisted5" version="5.0.0" file="emboss_5/emboss_btwisted.xml" /> + <tool id="EMBOSS: cai_custom6" version="5.0.0" file="emboss_5/emboss_cai_custom.xml" /> + <tool id="EMBOSS: cai6" version="5.0.0" file="emboss_5/emboss_cai.xml" /> + <tool id="EMBOSS: chaos7" version="5.0.0" file="emboss_5/emboss_chaos.xml" /> + <tool id="EMBOSS: charge8" version="5.0.0" file="emboss_5/emboss_charge.xml" /> + <tool id="EMBOSS: checktrans9" version="5.0.0" file="emboss_5/emboss_checktrans.xml" /> + <tool id="EMBOSS: chips10" version="5.0.0" file="emboss_5/emboss_chips.xml" /> + <tool id="EMBOSS: cirdna11" version="5.0.0" file="emboss_5/emboss_cirdna.xml" /> + <tool id="EMBOSS: codcmp12" version="5.0.0" file="emboss_5/emboss_codcmp.xml" /> + <tool id="EMBOSS: coderet13" version="5.0.0" file="emboss_5/emboss_coderet.xml" /> + <tool id="EMBOSS: compseq14" version="5.0.0" file="emboss_5/emboss_compseq.xml" /> + <tool id="EMBOSS: cpgplot15" version="5.0.0" file="emboss_5/emboss_cpgplot.xml" /> + <tool id="EMBOSS: cpgreport16" version="5.0.0" file="emboss_5/emboss_cpgreport.xml" /> + <tool id="EMBOSS: cusp17" version="5.0.0" file="emboss_5/emboss_cusp.xml" /> + <tool id="EMBOSS: cutseq18" version="5.0.0" file="emboss_5/emboss_cutseq.xml" /> + <tool id="EMBOSS: dan19" version="5.0.0" file="emboss_5/emboss_dan.xml" /> + <tool id="EMBOSS: degapseq20" version="5.0.0" file="emboss_5/emboss_degapseq.xml" /> + <tool id="EMBOSS: descseq21" version="5.0.0" file="emboss_5/emboss_descseq.xml" /> + <tool id="EMBOSS: diffseq22" version="5.0.0" file="emboss_5/emboss_diffseq.xml" /> + <tool id="EMBOSS: digest23" version="5.0.0" file="emboss_5/emboss_digest.xml" /> + <tool id="EMBOSS: dotmatcher24" version="5.0.0" file="emboss_5/emboss_dotmatcher.xml" /> + <tool id="EMBOSS: dotpath25" version="5.0.0" file="emboss_5/emboss_dotpath.xml" /> + <tool id="EMBOSS: dottup26" version="5.0.0" file="emboss_5/emboss_dottup.xml" /> + <tool id="EMBOSS: dreg27" version="5.0.0" file="emboss_5/emboss_dreg.xml" /> + <tool id="EMBOSS: einverted28" version="5.0.0" file="emboss_5/emboss_einverted.xml" /> + <tool id="EMBOSS: epestfind29" version="5.0.0" file="emboss_5/emboss_epestfind.xml" /> + <tool id="EMBOSS: equicktandem31" version="5.0.0" file="emboss_5/emboss_equicktandem.xml" /> + <tool id="EMBOSS: est2genome32" version="5.0.0" file="emboss_5/emboss_est2genome.xml" /> + <tool id="EMBOSS: etandem33" version="5.0.0" file="emboss_5/emboss_etandem.xml" /> + <tool id="EMBOSS: extractfeat34" version="5.0.0" file="emboss_5/emboss_extractfeat.xml" /> + <tool id="EMBOSS: extractseq35" version="5.0.0" file="emboss_5/emboss_extractseq.xml" /> + <tool id="EMBOSS: freak36" version="5.0.0" file="emboss_5/emboss_freak.xml" /> + <tool id="EMBOSS: fuzznuc37" version="5.0.0" file="emboss_5/emboss_fuzznuc.xml" /> + <tool id="EMBOSS: fuzzpro38" version="5.0.0" file="emboss_5/emboss_fuzzpro.xml" /> + <tool id="EMBOSS: fuzztran39" version="5.0.0" file="emboss_5/emboss_fuzztran.xml" /> + <tool id="EMBOSS: garnier40" version="5.0.0" file="emboss_5/emboss_garnier.xml" /> + <tool id="EMBOSS: geecee41" version="5.0.0" file="emboss_5/emboss_geecee.xml" /> + <tool id="EMBOSS: getorf42" version="5.0.0" file="emboss_5/emboss_getorf.xml" /> + <tool id="EMBOSS: helixturnhelix43" version="5.0.0" file="emboss_5/emboss_helixturnhelix.xml" /> + <tool id="EMBOSS: hmoment44" version="5.0.0" file="emboss_5/emboss_hmoment.xml" /> + <tool id="EMBOSS: iep45" version="5.0.0" file="emboss_5/emboss_iep.xml" /> + <tool id="EMBOSS: infoseq46" version="5.0.0" file="emboss_5/emboss_infoseq.xml" /> + <tool id="EMBOSS: isochore47" version="5.0.0" file="emboss_5/emboss_isochore.xml" /> + <tool id="EMBOSS: lindna48" version="5.0.0" file="emboss_5/emboss_lindna.xml" /> + <tool id="EMBOSS: marscan49" version="5.0.0" file="emboss_5/emboss_marscan.xml" /> + <tool id="EMBOSS: maskfeat50" version="5.0.0" file="emboss_5/emboss_maskfeat.xml" /> + <tool id="EMBOSS: maskseq51" version="5.0.0" file="emboss_5/emboss_maskseq.xml" /> + <tool id="EMBOSS: matcher52" version="5.0.0" file="emboss_5/emboss_matcher.xml" /> + <tool id="EMBOSS: megamerger53" version="5.0.0" file="emboss_5/emboss_megamerger.xml" /> + <tool id="EMBOSS: merger54" version="5.0.0" file="emboss_5/emboss_merger.xml" /> + <tool id="EMBOSS: msbar55" version="5.0.0" file="emboss_5/emboss_msbar.xml" /> + <tool id="EMBOSS: needle56" version="5.0.0" file="emboss_5/emboss_needle.xml" /> + <tool id="EMBOSS: newcpgreport57" version="5.0.0" file="emboss_5/emboss_newcpgreport.xml" /> + <tool id="EMBOSS: newcpgseek58" version="5.0.0" file="emboss_5/emboss_newcpgseek.xml" /> + <tool id="EMBOSS: newseq59" version="5.0.0" file="emboss_5/emboss_newseq.xml" /> + <tool id="EMBOSS: noreturn60" version="5.0.0" file="emboss_5/emboss_noreturn.xml" /> + <tool id="EMBOSS: notseq61" version="5.0.0" file="emboss_5/emboss_notseq.xml" /> + <tool id="EMBOSS: nthseq62" version="5.0.0" file="emboss_5/emboss_nthseq.xml" /> + <tool id="EMBOSS: octanol63" version="5.0.0" file="emboss_5/emboss_octanol.xml" /> + <tool id="EMBOSS: oddcomp64" version="5.0.0" file="emboss_5/emboss_oddcomp.xml" /> + <tool id="EMBOSS: palindrome65" version="5.0.0" file="emboss_5/emboss_palindrome.xml" /> + <tool id="EMBOSS: pasteseq66" version="5.0.0" file="emboss_5/emboss_pasteseq.xml" /> + <tool id="EMBOSS: patmatdb67" version="5.0.0" file="emboss_5/emboss_patmatdb.xml" /> + <tool id="EMBOSS: pepcoil68" version="5.0.0" file="emboss_5/emboss_pepcoil.xml" /> + <tool id="EMBOSS: pepinfo69" version="5.0.0" file="emboss_5/emboss_pepinfo.xml" /> + <tool id="EMBOSS: pepnet70" version="5.0.0" file="emboss_5/emboss_pepnet.xml" /> + <tool id="EMBOSS: pepstats71" version="5.0.0" file="emboss_5/emboss_pepstats.xml" /> + <tool id="EMBOSS: pepwheel72" version="5.0.0" file="emboss_5/emboss_pepwheel.xml" /> + <tool id="EMBOSS: pepwindow73" version="5.0.0" file="emboss_5/emboss_pepwindow.xml" /> + <tool id="EMBOSS: pepwindowall74" version="5.0.0" file="emboss_5/emboss_pepwindowall.xml" /> + <tool id="EMBOSS: plotcon75" version="5.0.0" file="emboss_5/emboss_plotcon.xml" /> + <tool id="EMBOSS: plotorf76" version="5.0.0" file="emboss_5/emboss_plotorf.xml" /> + <tool id="EMBOSS: polydot77" version="5.0.0" file="emboss_5/emboss_polydot.xml" /> + <tool id="EMBOSS: preg78" version="5.0.0" file="emboss_5/emboss_preg.xml" /> + <tool id="EMBOSS: prettyplot79" version="5.0.0" file="emboss_5/emboss_prettyplot.xml" /> + <tool id="EMBOSS: prettyseq80" version="5.0.0" file="emboss_5/emboss_prettyseq.xml" /> + <tool id="EMBOSS: primersearch81" version="5.0.0" file="emboss_5/emboss_primersearch.xml" /> + <tool id="EMBOSS: revseq82" version="5.0.0" file="emboss_5/emboss_revseq.xml" /> + <tool id="EMBOSS: seqmatchall83" version="5.0.0" file="emboss_5/emboss_seqmatchall.xml" /> + <tool id="EMBOSS: seqret84" version="5.0.0" file="emboss_5/emboss_seqret.xml" /> + <tool id="EMBOSS: showfeat85" version="5.0.0" file="emboss_5/emboss_showfeat.xml" /> + <tool id="EMBOSS: shuffleseq87" version="5.0.0" file="emboss_5/emboss_shuffleseq.xml" /> + <tool id="EMBOSS: sigcleave88" version="5.0.0" file="emboss_5/emboss_sigcleave.xml" /> + <tool id="EMBOSS: sirna89" version="5.0.0" file="emboss_5/emboss_sirna.xml" /> + <tool id="EMBOSS: sixpack90" version="5.0.0" file="emboss_5/emboss_sixpack.xml" /> + <tool id="EMBOSS: skipseq91" version="5.0.0" file="emboss_5/emboss_skipseq.xml" /> + <tool id="EMBOSS: splitter92" version="5.0.0" file="emboss_5/emboss_splitter.xml" /> + <tool id="EMBOSS: supermatcher95" version="5.0.0" file="emboss_5/emboss_supermatcher.xml" /> + <tool id="EMBOSS: syco96" version="5.0.0" file="emboss_5/emboss_syco.xml" /> + <tool id="EMBOSS: tcode97" version="5.0.0" file="emboss_5/emboss_tcode.xml" /> + <tool id="EMBOSS: textsearch98" version="5.0.0" file="emboss_5/emboss_textsearch.xml" /> + <tool id="EMBOSS: tmap99" version="5.0.0" file="emboss_5/emboss_tmap.xml" /> + <tool id="EMBOSS: tranalign100" version="5.0.0" file="emboss_5/emboss_tranalign.xml" /> + <tool id="EMBOSS: transeq101" version="5.0.0" file="emboss_5/emboss_transeq.xml" /> + <tool id="EMBOSS: trimest102" version="5.0.0" file="emboss_5/emboss_trimest.xml" /> + <tool id="EMBOSS: trimseq103" version="5.0.0" file="emboss_5/emboss_trimseq.xml" /> + <tool id="EMBOSS: twofeat104" version="5.0.0" file="emboss_5/emboss_twofeat.xml" /> + <tool id="EMBOSS: union105" version="5.0.0" file="emboss_5/emboss_union.xml" /> + <tool id="EMBOSS: vectorstrip106" version="5.0.0" file="emboss_5/emboss_vectorstrip.xml" /> + <tool id="EMBOSS: water107" version="5.0.0" file="emboss_5/emboss_water.xml" /> + <tool id="EMBOSS: wobble108" version="5.0.0" file="emboss_5/emboss_wobble.xml" /> + <tool id="EMBOSS: wordcount109" version="5.0.0" file="emboss_5/emboss_wordcount.xml" /> + <tool id="EMBOSS: wordmatch110" version="5.0.0" file="emboss_5/emboss_wordmatch.xml" /></repository></toolshed> diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0003_tools.xml --- a/scripts/migrate_tools/0003_tools.xml +++ b/scripts/migrate_tools/0003_tools.xml @@ -1,6 +1,6 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="freebayes" description="Galaxy Freebayes Bayesian genetic variant detector tool" changeset_revision="213a3d6b579a"> - <tool id="freebayes" version="0.0.2 " file="freebayes.xml" /> + <tool id="freebayes" version="0.0.2 " file="variant_detection/freebayes.xml" /></repository></toolshed> diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0004_tools.xml --- a/scripts/migrate_tools/0004_tools.xml +++ b/scripts/migrate_tools/0004_tools.xml @@ -2,11 +2,11 @@ <toolshed name="toolshed.g2.bx.psu.edu"><repository name="blast_datatypes" description="Datatypes for BLAST" changeset_revision="e1c29f302301" /><repository name="ncbi_blast_plus" description="Galaxy wrappers for NCBI BLAST+" changeset_revision="d375502056f1"> - <tool id="blastxml_to_tabular" version="0.0.8" file="blastxml_to_tabular.xml"/> - <tool id="ncbi_blastn_wrapper" version="0.0.11" file="ncbi_blastn_wrapper.xml"/> - <tool id="ncbi_blastp_wrapper" version="0.0.11" file="ncbi_blastp_wrapper.xml"/> - <tool id="ncbi_blastx_wrapper" version="0.0.11" file="ncbi_blastx_wrapper.xml"/> - <tool id="ncbi_tblastn_wrapper" version="0.0.11" file="ncbi_tblastn_wrapper.xml"/> - <tool id="ncbi_tblastx_wrapper" version="0.0.11" file="ncbi_tblastx_wrapper.xml"/> + <tool id="blastxml_to_tabular" version="0.0.8" file="ncbi_blast_plus/blastxml_to_tabular.xml"/> + <tool id="ncbi_blastn_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_blastn_wrapper.xml"/> + <tool id="ncbi_blastp_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_blastp_wrapper.xml"/> + <tool id="ncbi_blastx_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_blastx_wrapper.xml"/> + <tool id="ncbi_tblastn_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml"/> + <tool id="ncbi_tblastx_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml"/></repository></toolshed> diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0005_tools.xml --- a/scripts/migrate_tools/0005_tools.xml +++ b/scripts/migrate_tools/0005_tools.xml @@ -1,7 +1,7 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="bwa_wrappers" description="Galaxy wrappers for the BWA short read aligner." changeset_revision="ffa8aaa14f7c"> - <tool id="bwa_wrapper" version="1.2.3" file="bwa_wrapper.xml"/> - <tool id="bwa_color_wrapper" version="1.0.2" file="bwa_color_wrapper.xml"/> + <tool id="bwa_wrapper" version="1.2.3" file="sr_mapping/bwa_wrapper.xml"/> + <tool id="bwa_color_wrapper" version="1.0.2" file="sr_mapping/bwa_color_wrapper.xml"/></repository></toolshed> diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0006_tools.xml --- a/scripts/migrate_tools/0006_tools.xml +++ b/scripts/migrate_tools/0006_tools.xml @@ -1,18 +1,18 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="picard" description="Galaxy wrappers for the Picard SAM/BAM manipulation tools." changeset_revision="e0232cbac965"> - <tool id="picard_FastqToSam" version="1.56.0" file="picard_FastqToSam.xml" /> - <tool id="picard_SamToFastq" version="1.56.1" file="picard_SamToFastq.xml" /> - <tool id="picard_BamIndexStats" version="1.56.0" file="picard_BamIndexStats.xml" /> - <tool id="PicardASMetrics" version="1.56.0" file="rgPicardASMetrics.xml" /> - <tool id="PicardGCBiasMetrics" version="1.56.0" file="rgPicardGCBiasMetrics.xml" /> - <tool id="rgEstLibComp" version="1.56.0" file="rgPicardLibComplexity.xml" /> - <tool id="PicardInsertSize" version="1.56.0" file="rgPicardInsertSize.xml" /> - <tool id="PicardHsMetrics" version="1.56.0" file="rgPicardHsMetrics.xml" /> - <tool id="picard_ARRG" version="1.56.0" file="picard_AddOrReplaceReadGroups.xml" /> - <tool id="picard_ReorderSam" version="1.56.0" file="picard_ReorderSam.xml" /> - <tool id="picard_ReplaceSamHeader" version="1.56.0" file="picard_ReplaceSamHeader.xml" /> - <tool id="rgPicFixMate" version="1.56.0" file="rgPicardFixMate.xml" /> - <tool id="rgPicardMarkDups" version="1.56.0" file="rgPicardMarkDups.xml" /> + <tool id="picard_FastqToSam" version="1.56.0" file="picard/picard_FastqToSam.xml" /> + <tool id="picard_SamToFastq" version="1.56.1" file="picard/picard_SamToFastq.xml" /> + <tool id="picard_BamIndexStats" version="1.56.0" file="picard/picard_BamIndexStats.xml" /> + <tool id="PicardASMetrics" version="1.56.0" file="picard/rgPicardASMetrics.xml" /> + <tool id="PicardGCBiasMetrics" version="1.56.0" file="picard/rgPicardGCBiasMetrics.xml" /> + <tool id="rgEstLibComp" version="1.56.0" file="picard/rgPicardLibComplexity.xml" /> + <tool id="PicardInsertSize" version="1.56.0" file="picard/rgPicardInsertSize.xml" /> + <tool id="PicardHsMetrics" version="1.56.0" file="picard/rgPicardHsMetrics.xml" /> + <tool id="picard_ARRG" version="1.56.0" file="picard/picard_AddOrReplaceReadGroups.xml" /> + <tool id="picard_ReorderSam" version="1.56.0" file="picard/picard_ReorderSam.xml" /> + <tool id="picard_ReplaceSamHeader" version="1.56.0" file="picard/picard_ReplaceSamHeader.xml" /> + <tool id="rgPicFixMate" version="1.56.0" file="picard/rgPicardFixMate.xml" /> + <tool id="rgPicardMarkDups" version="1.56.0" file="picard/rgPicardMarkDups.xml" /></repository></toolshed> diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0007_tools.xml --- a/scripts/migrate_tools/0007_tools.xml +++ b/scripts/migrate_tools/0007_tools.xml @@ -1,15 +1,15 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="bowtie_wrappers" description="Galaxy wrappers for the Bowtie short read mapping tools." changeset_revision="0c7e4eadfb3c"> - <tool id="bowtie_wrapper" version="1.1.2" file="bowtie_wrapper.xml" /> + <tool id="bowtie_wrapper" version="1.1.2" file="sr_mapping/bowtie_wrapper.xml" /></repository><repository name="bowtie_color_wrappers" description="Galaxy wrappers for the Bowtie short read mapping tools on color space reads" changeset_revision="fd0914e451c5"> - <tool id="bowtie_color_wrapper" version="1.1.2" file="bowtie_color_wrapper.xml" /> + <tool id="bowtie_color_wrapper" version="1.1.2" file="sr_mapping/bowtie_color_wrapper.xml" /></repository><repository name="lastz" description="Galaxy wrappers for the Lastz alignment tool" changeset_revision="0801f8207d30"> - <tool id="lastz_wrapper_2" version="1.1.2" file="lastz_wrapper.xml" /> + <tool id="lastz_wrapper_2" version="1.1.2" file="sr_mapping/lastz_wrapper.xml" /></repository><repository name="lastz_paired_reads" description="Galaxy wrapper for the Lastz alignment tool on paired reads" changeset_revision="96825cee5c25"> - <tool id="lastz_paired_reads_wrapper" version="1.1.1" file="lastz_paired_reads_wrapper.xml" /> + <tool id="lastz_paired_reads_wrapper" version="1.1.1" file="sr_mapping/lastz_paired_reads_wrapper.xml" /></repository></toolshed> diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0008_tools.xml --- a/scripts/migrate_tools/0008_tools.xml +++ b/scripts/migrate_tools/0008_tools.xml @@ -1,147 +1,147 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository owner="devteam" changeset_revision="dc20f447c0e2" name="bam_to_sam" description="Galaxy wrappers for the tool BAM-to-SAM: converts BAM format to SAM format"> - <tool id="bam_to_sam" version="1.0.3" file="bam_to_sam.xml" /> + <tool id="bam_to_sam" version="1.0.3" file="samtools/bam_to_sam.xml" /></repository><repository owner="devteam" changeset_revision="586c1f0e1515" name="categorize_elements_satisfying_criteria" description="Galaxy wrappers for the tool Categorize Elements: satisfying criteria"> - <tool id="categorize_elements_satisfying_criteria" version="1.0.0" file="categorize_elements_satisfying_criteria.xml" /> + <tool id="categorize_elements_satisfying_criteria" version="1.0.0" file="regVariation/categorize_elements_satisfying_criteria.xml" /></repository><repository owner="devteam" changeset_revision="acc3dc5d26e3" name="compute_motif_frequencies_for_all_motifs" description="Galaxy wrappers for the tool Compute Motif Frequencies For All Motifs: motif by motif"> - <tool id="compute_motif_frequencies_for_all_motifs" version="1.0.0" file="compute_motif_frequencies_for_all_motifs.xml" /> + <tool id="compute_motif_frequencies_for_all_motifs" version="1.0.0" file="regVariation/compute_motif_frequencies_for_all_motifs.xml" /></repository><repository owner="devteam" changeset_revision="46325357b948" name="compute_motifs_frequency" description="Galaxy wrappers for the tool Compute Motif Frequencies: in indel flanking regions"> - <tool id="compute_motifs_frequency" version="1.0.0" file="compute_motifs_frequency.xml" /> + <tool id="compute_motifs_frequency" version="1.0.0" file="regVariation/compute_motifs_frequency.xml" /></repository><repository owner="devteam" changeset_revision="4a32700dcaa2" name="ctd_batch" description="Galaxy wrappers for the tool CTD: analysis of chemicals, diseases, or genes"> - <tool id="ctdBatch_1" version="1.0.0" file="ctd.xml" /> + <tool id="ctdBatch_1" version="1.0.0" file="phenotype_association/ctd.xml" /></repository><repository owner="devteam" changeset_revision="9a3f7a890da6" name="cuffcompare" description="Galaxy wrappers for the Cuffcompare tool."> - <tool id="cuffcompare" version="0.0.5" file="cuffcompare_wrapper.xml" /> + <tool id="cuffcompare" version="0.0.5" file="ngs_rna/cuffcompare_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="0dabb2ed6eb1" name="cuffdiff" description="Galaxy wrappers for the Cuffdiff tool."> - <tool id="cuffdiff" version="0.0.6" file="cuffdiff_wrapper.xml" /> + <tool id="cuffdiff" version="0.0.6" file="ngs_rna/cuffdiff_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="b01956f26c36" name="cufflinks" description="Galaxy wrappers for the Cufflinks tool."> - <tool id="cufflinks" version="0.0.6" file="cufflinks_wrapper.xml" /> + <tool id="cufflinks" version="0.0.6" file="ngs_rna/cufflinks_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="fdc55fd74f78" name="cuffmerge" description="Galaxy wrappers for the Cuffmerge tool."> - <tool id="cuffmerge" version="0.0.5" file="cuffmerge_wrapper.xml" /> + <tool id="cuffmerge" version="0.0.5" file="ngs_rna/cuffmerge_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="f16000dc644b" name="delete_overlapping_indels" description="Galaxy wrappers for the tool Delete Overlapping Indels: from a chromosome indels file"> - <tool id="delete_overlapping_indels" version="1.0.0" file="delete_overlapping_indels.xml" /> + <tool id="delete_overlapping_indels" version="1.0.0" file="regVariation/delete_overlapping_indels.xml" /></repository><repository owner="devteam" changeset_revision="de839553d2a2" name="divide_pg_snp" description="Galaxy wrappers for the tool Separate pgSnp alleles: into columns"> - <tool id="dividePgSnp" version="1.0.0" file="dividePgSnpAlleles.xml" /> + <tool id="dividePgSnp" version="1.0.0" file="phenotype_association/dividePgSnpAlleles.xml" /></repository><repository owner="devteam" changeset_revision="063ecbe59faf" name="draw_stacked_barplots" description="Galaxy wrappers for the tool Draw Stacked Bar Plots: for different categories and different criteria"> - <tool id="draw_stacked_barplots" version="1.0.0" file="draw_stacked_barplots.xml" /> + <tool id="draw_stacked_barplots" version="1.0.0" file="regVariation/draw_stacked_barplots.xml" /></repository><repository owner="devteam" changeset_revision="f2ab5b44870d" name="fasta_clipping_histogram" description="Galaxy wrappers for the tool Length Distribution chart"> - <tool id="cshl_fasta_clipping_histogram" version="1.0.0" file="fasta_clipping_histogram.xml" /> + <tool id="cshl_fasta_clipping_histogram" version="1.0.0" file="fastx_toolkit/fasta_clipping_histogram.xml" /></repository><repository owner="devteam" changeset_revision="8f0ae92440b8" name="fasta_formatter" description="Galaxy wrappers for the tool FASTA Width: formatter"> - <tool id="cshl_fasta_formatter" version="1.0.0" file="fasta_formatter.xml" /> + <tool id="cshl_fasta_formatter" version="1.0.0" file="fastx_toolkit/fasta_formatter.xml" /></repository><repository owner="devteam" changeset_revision="4b41e3076a50" name="fasta_nucleotide_changer" description="Galaxy wrappers for the tool RNA/DNA: converter"> - <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" file="fasta_nucleotide_changer.xml" /> + <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" file="fastx_toolkit/fasta_nucleotide_changer.xml" /></repository><repository owner="devteam" changeset_revision="e359ce20fbd9" name="fastq_quality_boxplot" description="Galaxy wrappers for the tool Draw quality score boxplot"> - <tool id="cshl_fastq_quality_boxplot" version="1.0.0" file="fastq_quality_boxplot.xml" /> + <tool id="cshl_fastq_quality_boxplot" version="1.0.0" file="fastx_toolkit/fastq_quality_boxplot.xml" /></repository><repository owner="devteam" changeset_revision="b87c74b61d81" name="fastq_quality_converter" description="Galaxy wrappers for the tool Quality format converter: (ASCII-Numeric)"> - <tool id="cshl_fastq_quality_converter" version="1.0.0" file="fastq_quality_converter.xml" /> + <tool id="cshl_fastq_quality_converter" version="1.0.0" file="fastx_toolkit/fastq_quality_converter.xml" /></repository><repository owner="devteam" changeset_revision="b145b9b26648" name="fastq_quality_filter" description="Galaxy wrappers for the Filter by quality tool."> - <tool id="cshl_fastq_quality_filter" version="1.0.0" file="fastq_quality_filter.xml" /> + <tool id="cshl_fastq_quality_filter" version="1.0.0" file="fastx_toolkit/fastq_quality_filter.xml" /></repository><repository owner="devteam" changeset_revision="04614cf6ed39" name="fastq_to_fasta" description="Galaxy wrappers for the tool FASTQ to FASTA: converter"> - <tool id="cshl_fastq_to_fasta" version="1.0.0" file="fastq_to_fasta.xml" /> + <tool id="cshl_fastq_to_fasta" version="1.0.0" file="fastx_toolkit/fastq_to_fasta.xml" /></repository><repository owner="devteam" changeset_revision="7f9660a246c0" name="fastx_artifacts_filter" description="Galaxy wrappers for the Remove sequencing artifacts tool."> - <tool id="cshl_fastx_artifacts_filter" version="1.0.0" file="fastx_artifacts_filter.xml" /> + <tool id="cshl_fastx_artifacts_filter" version="1.0.0" file="fastx_toolkit/fastx_artifacts_filter.xml" /></repository><repository owner="devteam" changeset_revision="a12850d0559b" name="fastx_barcode_splitter" description="Galaxy wrappers for the Barcode Splitter tool."> - <tool id="cshl_fastx_barcode_splitter" version="1.0.0" file="fastx_barcode_splitter.xml" /> + <tool id="cshl_fastx_barcode_splitter" version="1.0.0" file="fastx_toolkit/fastx_barcode_splitter.xml" /></repository><repository owner="devteam" changeset_revision="2fe2d2b9e8e4" name="fastx_clipper" description="Galaxy wrappers for the tool Clip: adapter sequences"> - <tool id="cshl_fastx_clipper" version="1.0.1" file="fastx_clipper.xml" /> + <tool id="cshl_fastx_clipper" version="1.0.1" file="fastx_toolkit/fastx_clipper.xml" /></repository><repository owner="devteam" changeset_revision="e942fd3a76a5" name="fastx_collapser" description="Galaxy wrappers for the tool Collapse: sequences"> - <tool id="cshl_fastx_collapser" version="1.0.0" file="fastx_collapser.xml" /> + <tool id="cshl_fastx_collapser" version="1.0.0" file="fastx_toolkit/fastx_collapser.xml" /></repository><repository owner="devteam" changeset_revision="bcc5424a4a3c" name="fastx_nucleotides_distribution" description="Galaxy wrappers for the Draw nucleotides distribution chart tool."> - <tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" file="fastx_nucleotides_distribution.xml" /> + <tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" 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file="fastx_reverse_complement.xml" /> + <tool id="cshl_fastx_reverse_complement" version="1.0.0" file="fastx_toolkit/fastx_reverse_complement.xml" /></repository><repository owner="devteam" changeset_revision="9cb372481a71" name="fastx_trimmer" description="Galaxy wrappers for the Trim sequences tool."> - <tool id="cshl_fastx_trimmer" version="1.0.0" file="fastx_trimmer.xml" /> + <tool id="cshl_fastx_trimmer" version="1.0.0" file="fastx_toolkit/fastx_trimmer.xml" /></repository><repository owner="devteam" changeset_revision="64133669255f" name="hgv_fundo" description="Galaxy wrappers for the tool FunDO: human genes associated with disease terms"> - <tool id="hgv_funDo" version="1.0.0" file="funDo.xml" /> + <tool id="hgv_funDo" version="1.0.0" file="phenotype_association/funDo.xml" /></repository><repository owner="devteam" changeset_revision="0e80ffa5b7f7" name="hgv_hilbertvis" description="Galaxy wrappers for the tool HVIS: visualization of genomic data with the Hilbert curve"> - 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tool."> - <tool id="t_test_two_samples" version="1.0.0" file="t_test_two_samples.xml" /> + <tool id="t_test_two_samples" version="1.0.0" file="regVariation/t_test_two_samples.xml" /></repository><repository owner="devteam" changeset_revision="acf952549b53" name="xy_plot" description="Galaxy wrappers for the tool Plotting tool: for multiple series and graph types"> - <tool id="XY_Plot_1" version="1.0.1" file="xy_plot.xml" /> + <tool id="XY_Plot_1" version="1.0.1" file="plotting/xy_plot.xml" /></repository></toolshed> \ No newline at end of file diff -r f58179ab488879a1a54821e98b4c65c048fa2fd6 -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 scripts/migrate_tools/0009_tools.xml --- a/scripts/migrate_tools/0009_tools.xml +++ b/scripts/migrate_tools/0009_tools.xml @@ -1,132 +1,132 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository owner="devteam" changeset_revision="96d2e31a3938" name="bowtie2" description="Bowtie2"> - <tool id="bowtie2" version="0.2" 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converter"> - <tool id="tabular_to_fastq" version="1.0.0" file="tabular_to_fastq.xml" /> + <tool id="tabular_to_fastq" version="1.0.0" file="fastq/tabular_to_fastq.xml" /></repository><repository owner="devteam" changeset_revision="1030acbecce6" name="tophat" description="Find splice junctions using RNA-seq data"> - <tool id="tophat" version="1.5.0" file="tophat_wrapper.xml" /> + <tool id="tophat" version="1.5.0" file="ngs_rna/tophat_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="ffa30bedbee3" name="tophat2" description="Gapped-read mapper for RNA-seq data"> - <tool id="tophat2" version="0.6" file="tophat2_wrapper.xml" /> + <tool id="tophat2" version="0.6" file="ngs_rna/tophat2_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="b001b50f2009" name="vcf_annotate" description="Annotate a VCF file (dbSNP, hapmap)"> - <tool id="vcf_annotate" version="1.0.0" file="annotate.xml" /> + <tool id="vcf_annotate" version="1.0.0" file="vcf_tools/annotate.xml" /></repository><repository owner="devteam" changeset_revision="76ad0b7865b9" name="vcf_extract" description="Extract reads from a specified region"> - <tool id="vcf_extract" version="1.0.0" file="extract.xml" /> + <tool id="vcf_extract" version="1.0.0" file="vcf_tools/extract.xml" /></repository><repository owner="devteam" changeset_revision="da1a6f33b504" name="vcf_filter" description="Filter a VCF file"> - <tool id="vcf_filter" version="1.0.0" file="filter.xml" /> + <tool id="vcf_filter" version="1.0.0" file="vcf_tools/filter.xml" /></repository><repository owner="devteam" changeset_revision="9d162bde4113" name="vcf_intersect" description="Generate the intersection of two VCF files"><tool id="vcf_intersect" version="1.0.0" file="vcf_tools/intersect.xml" /></repository><repository owner="devteam" changeset_revision="66253fc0a69b" name="weblogo3" description="Sequence Logo generator for fasta (eg Clustal alignments)"> - <tool id="rgweblogo3" version="0.4" file="rgWebLogo3.xml" /> + <tool id="rgweblogo3" version="0.4" file="rgenetics/rgWebLogo3.xml" /></repository></toolshed> \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/d20888b2d96c/ Changeset: d20888b2d96c Branch: stable User: davebgx Date: 2014-02-21 00:01:05 Summary: Fix path for bowtie2. Affected #: 1 file diff -r ba001f4c03264d9c244ce27a7472757e03ff3bd5 -r d20888b2d96c8a021871a4252b5cc74e09578f07 scripts/migrate_tools/0009_tools.xml --- a/scripts/migrate_tools/0009_tools.xml +++ b/scripts/migrate_tools/0009_tools.xml @@ -1,7 +1,7 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository owner="devteam" changeset_revision="96d2e31a3938" name="bowtie2" description="Bowtie2"> - <tool id="bowtie2" version="0.2" file="ngs_rna/bowtie2_wrapper.xml" /> + <tool id="bowtie2" version="0.2" file="sr_mapping/bowtie2_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="a0c8dc671a23" name="ccat" description="Control-based ChIP-seq Analysis Tool"><tool id="peakcalling_ccat" version="0.0.1" file="peak_calling/ccat_wrapper.xml" /> https://bitbucket.org/galaxy/galaxy-central/commits/6f9d716d0009/ Changeset: 6f9d716d0009 User: davebgx Date: 2014-02-21 18:38:04 Summary: Merge stable. Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.