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More interface changes and updates to tool_conf.xml.main and tool_conf.xml.sample

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This commit is contained in:
Anton Nekrutenko
2007-07-17 15:17:11 +00:00
parent 8bc14e03fa
commit e130de1a26
6 changed files with 71 additions and 436 deletions
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templates/masthead.tmpl
+3 -2
View File
@@ -21,8 +21,9 @@
*#
Info: <a href="mailto:galaxy-bugs@bx.psu.edu">report bugs</a>
| <a target="_blank" href="http://www.bx.psu.edu/cgi-bin/trac.cgi">wiki</a>
| <a target="_blank" href="http://www.bx.psu.edu/cgi-bin/trac.cgi/wiki/ScreenCasts">screencasts</a>
| <a target="_blank" href="http://g2.trac.bx.psu.edu/">wiki</a>
| <a target="_blank" href="http://g2.trac.bx.psu.edu/wiki/ScreenCasts">screencasts</a>
| <a target="_blank" href="http://g2.trac.bx.psu.edu/blog">blog</a>
<!-- | <a target="mainframe" href="/static/index_frame_tools.html">tools</a>
| <a target="mainframe" href="/static/index_frame_history.html">history</a> -->
&nbsp;&nbsp;&nbsp;
tool_conf.xml.main
+10 -195
View File
@@ -81,10 +81,10 @@
<tool file="extract/interval_maf_to_merged_fasta_user.xml" />
<!-- <tool file="extract/genebed_maf_to_fasta.xml"/>
<tool file="extract/genebed_maf_to_fasta_user.xml"/>
<tool file="filters/maf/maf_stats.xml"/>
<tool file="filters/maf/maf_stats.xml"/> -->
<tool file="filters/maf/maf_limit_to_species.xml"/>
<tool file="filters/maf/maf_limit_size.xml"/>
<tool file="filters/maf/maf_by_block_number.xml"/> -->
<tool file="filters/maf/maf_by_block_number.xml"/>
</section>
<section name="Get Genomic Scores" id="scores">
<tool file="stats/wiggle_to_simple.xml" />
@@ -111,12 +111,17 @@
<section name="Graph/Display Data" id="plots">
<tool file="plotting/histogram2.xml" />
<tool file="plotting/scatterplot.xml" />
<!-- <tool file="plotting/xy_plot.xml" /> -->
<tool file="plotting/xy_plot.xml" />
<tool file="visualization/GMAJ.xml" />
<!-- <tool file="visualization/LAJ.xml" /> -->
<!-- <tool file="data_source/show_in_ucsc.xml" />
<tool file="visualization/build_ucsc_custom_track.xml" /> -->
<!-- <tool file="data_source/show_in_ucsc.xml" /> -->
<tool file="visualization/build_ucsc_custom_track.xml" />
</section>
<section name="Evolution: HyPhy" id="hyphy">
<tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
<tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
<!-- <tool file="hyphy/hyphy_dnds_wrapper.xml" /> -->
</section>
<section name="EMBOSS" id="EMBOSSLite">
<tool file="emboss/emboss_cai.xml" />
<tool file="emboss/emboss_cai_custom.xml" />
@@ -174,194 +179,4 @@
<tool file="emboss/emboss_charge.xml" />
<tool file="emboss/emboss_checktrans.xml" />
</section>
<!--
<section name="Run EMBOSS nucleotide" id="EMBOSSnucleotide">
<tool file="emboss/emboss_biosed.xml" />
<tool file="emboss/emboss_btwisted.xml" />
<tool file="emboss/emboss_cai.xml" />
<tool file="emboss/emboss_chaos.xml" />
<tool file="emboss/emboss_chips.xml" />
<tool file="emboss/emboss_codcmp.xml" />
<tool file="emboss/emboss_coderet.xml" />
<tool file="emboss/emboss_compseq.xml" />
<tool file="emboss/emboss_cpgplot.xml" />
<tool file="emboss/emboss_cpgreport.xml" />
<tool file="emboss/emboss_cusp.xml" />
<tool file="emboss/emboss_cutseq.xml" />
<tool file="emboss/emboss_dan.xml" />
<tool file="emboss/emboss_degapseq.xml" />
<tool file="emboss/emboss_descseq.xml" />
<tool file="emboss/emboss_diffseq.xml" />
<tool file="emboss/emboss_dotmatcher.xml" />
<tool file="emboss/emboss_dotpath.xml" />
<tool file="emboss/emboss_dottup.xml" />
<tool file="emboss/emboss_einverted.xml" />
<tool file="emboss/emboss_equicktandem.xml" />
<tool file="emboss/emboss_est2genome.xml" />
<tool file="emboss/emboss_etandem.xml" />
<tool file="emboss/emboss_extractfeat.xml" />
<tool file="emboss/emboss_extractseq.xml" />
<tool file="emboss/emboss_freak.xml" />
<tool file="emboss/emboss_fuzznuc.xml" />
<tool file="emboss/emboss_fuzztran.xml" />
<tool file="emboss/emboss_geecee.xml" />
<tool file="emboss/emboss_getorf.xml" />
<tool file="emboss/emboss_helixturnhelix.xml" />
<tool file="emboss/emboss_infoseq.xml" />
<tool file="emboss/emboss_isochore.xml" />
<tool file="emboss/emboss_marscan.xml" />
<tool file="emboss/emboss_maskfeat.xml" />
<tool file="emboss/emboss_maskseq.xml" />
<tool file="emboss/emboss_matcher.xml" />
<tool file="emboss/emboss_megamerger.xml" />
<tool file="emboss/emboss_merger.xml" />
<tool file="emboss/emboss_msbar.xml" />
<tool file="emboss/emboss_needle.xml" />
<tool file="emboss/emboss_newcpgreport.xml" />
<tool file="emboss/emboss_newcpgseek.xml" />
<tool file="emboss/emboss_newseq.xml" />
<tool file="emboss/emboss_noreturn.xml" />
<tool file="emboss/emboss_notseq.xml" />
<tool file="emboss/emboss_nthseq.xml" />
<tool file="emboss/emboss_palindrome.xml" />
<tool file="emboss/emboss_pasteseq.xml" />
<tool file="emboss/emboss_plotorf.xml" />
<tool file="emboss/emboss_polydot.xml" />
<tool file="emboss/emboss_prettyseq.xml" />
<tool file="emboss/emboss_primersearch.xml" />
<tool file="emboss/emboss_revseq.xml" />
<tool file="emboss/emboss_seqmatchall.xml" />
<tool file="emboss/emboss_seqret.xml" />
<tool file="emboss/emboss_showfeat.xml" />
<tool file="emboss/emboss_showorf.xml" />
<tool file="emboss/emboss_shuffleseq.xml" />
<tool file="emboss/emboss_sirna.xml" />
<tool file="emboss/emboss_sixpack.xml" />
<tool file="emboss/emboss_skipseq.xml" />
<tool file="emboss/emboss_splitter.xml" />
<tool file="emboss/emboss_stretcher.xml" />
<tool file="emboss/emboss_stssearch.xml" />
<tool file="emboss/emboss_supermatcher.xml" />
<tool file="emboss/emboss_syco.xml" />
<tool file="emboss/emboss_tcode.xml" />
<tool file="emboss/emboss_textsearch.xml" />
<tool file="emboss/emboss_tranalign.xml" />
<tool file="emboss/emboss_transeq.xml" />
<tool file="emboss/emboss_trimest.xml" />
<tool file="emboss/emboss_trimseq.xml" />
<tool file="emboss/emboss_twofeat.xml" />
<tool file="emboss/emboss_union.xml" />
<tool file="emboss/emboss_vectorstrip.xml" />
<tool file="emboss/emboss_water.xml" />
<tool file="emboss/emboss_wobble.xml" />
<tool file="emboss/emboss_wordcount.xml" />
<tool file="emboss/emboss_wordmatch.xml" />
</section>
<section name="Run EMBOSS protein" id="EMBOSSprotein">
<tool file="emboss/emboss_antigenic.xml" />
<tool file="emboss/emboss_backtranseq.xml" />
<tool file="emboss/emboss_biosed.xml" />
<tool file="emboss/emboss_chaos.xml" />
<tool file="emboss/emboss_charge.xml" />
<tool file="emboss/emboss_checktrans.xml" />
<tool file="emboss/emboss_coderet.xml" />
<tool file="emboss/emboss_compseq.xml" />
<tool file="emboss/emboss_cutseq.xml" />
<tool file="emboss/emboss_degapseq.xml" />
<tool file="emboss/emboss_descseq.xml" />
<tool file="emboss/emboss_diffseq.xml" />
<tool file="emboss/emboss_digest.xml" />
<tool file="emboss/emboss_dotmatcher.xml" />
<tool file="emboss/emboss_dotpath.xml" />
<tool file="emboss/emboss_dottup.xml" />
<tool file="emboss/emboss_epestfind.xml" />
<tool file="emboss/emboss_extractfeat.xml" />
<tool file="emboss/emboss_extractseq.xml" />
<tool file="emboss/emboss_freak.xml" />
<tool file="emboss/emboss_fuzzpro.xml" />
<tool file="emboss/emboss_garnier.xml" />
<tool file="emboss/emboss_hmoment.xml" />
<tool file="emboss/emboss_iep.xml" />
<tool file="emboss/emboss_infoseq.xml" />
<tool file="emboss/emboss_maskfeat.xml" />
<tool file="emboss/emboss_maskseq.xml" />
<tool file="emboss/emboss_matcher.xml" />
<tool file="emboss/emboss_msbar.xml" />
<tool file="emboss/emboss_needle.xml" />
<tool file="emboss/emboss_newseq.xml" />
<tool file="emboss/emboss_noreturn.xml" />
<tool file="emboss/emboss_notseq.xml" />
<tool file="emboss/emboss_nthseq.xml" />
<tool file="emboss/emboss_octanol.xml" />
<tool file="emboss/emboss_oddcomp.xml" />
<tool file="emboss/emboss_pasteseq.xml" />
<tool file="emboss/emboss_patmatdb.xml" />
<tool file="emboss/emboss_pepcoil.xml" />
<tool file="emboss/emboss_pepinfo.xml" />
<tool file="emboss/emboss_pepstats.xml" />
<tool file="emboss/emboss_pepwheel.xml" />
<tool file="emboss/emboss_pepwindow.xml" />
<tool file="emboss/emboss_pepwindowall.xml" />
<tool file="emboss/emboss_polydot.xml" />
<tool file="emboss/emboss_seqmatchall.xml" />
<tool file="emboss/emboss_seqret.xml" />
<tool file="emboss/emboss_showfeat.xml" />
<tool file="emboss/emboss_shuffleseq.xml" />
<tool file="emboss/emboss_sigcleave.xml" />
<tool file="emboss/emboss_skipseq.xml" />
<tool file="emboss/emboss_splitter.xml" />
<tool file="emboss/emboss_stretcher.xml" />
<tool file="emboss/emboss_supermatcher.xml" />
<tool file="emboss/emboss_textsearch.xml" />
<tool file="emboss/emboss_tmap.xml" />
<tool file="emboss/emboss_tranalign.xml" />
<tool file="emboss/emboss_trimseq.xml" />
<tool file="emboss/emboss_twofeat.xml" />
<tool file="emboss/emboss_union.xml" />
<tool file="emboss/emboss_water.xml" />
<tool file="emboss/emboss_wordmatch.xml" />
</section>
-->
<!--
<section id="ePHYLIP" name="Run ePHYLIP">
<tool file="emboss/phylip/emboss_eclique.xml" />
<tool file="emboss/phylip/emboss_econsense.xml" />
<tool file="emboss/phylip/emboss_econtml.xml" />
<tool file="emboss/phylip/emboss_econtrast.xml" />
<tool file="emboss/phylip/emboss_ednacomp.xml" />
<tool file="emboss/phylip/emboss_ednadist.xml" />
<tool file="emboss/phylip/emboss_ednainvar.xml" />
<tool file="emboss/phylip/emboss_ednaml.xml" />
<tool file="emboss/phylip/emboss_ednamlk.xml" />
<tool file="emboss/phylip/emboss_ednapars.xml" />
<tool file="emboss/phylip/emboss_ednapenny.xml" />
<tool file="emboss/phylip/emboss_edollop.xml" />
<tool file="emboss/phylip/emboss_edolpenny.xml" />
<tool file="emboss/phylip/emboss_efactor.xml" />
<tool file="emboss/phylip/emboss_efitch.xml" />
<tool file="emboss/phylip/emboss_egendist.xml" />
<tool file="emboss/phylip/emboss_ekitsch.xml" />
<tool file="emboss/phylip/emboss_emix.xml" />
<tool file="emboss/phylip/emboss_eneighbor.xml" />
<tool file="emboss/phylip/emboss_epenny.xml" />
<tool file="emboss/phylip/emboss_eprotdist.xml" />
<tool file="emboss/phylip/emboss_eprotpars.xml" />
<tool file="emboss/phylip/emboss_erestml.xml" />
<tool file="emboss/phylip/emboss_eseqboot.xml" />
</section>
-->
<!-- <section name="PHYLIP" id="phylipnew">
<tool file="emboss/phylipnew/emboss_fdnadist.xml" />
<tool file="emboss/phylipnew/emboss_fdnapars.xml" />
<tool file="emboss/phylipnew/emboss_fdrawgram.xml" />
<tool file="emboss/phylipnew/emboss_ffitch.xml" />
<tool file="emboss/phylipnew/emboss_fseqboot.xml" />
<tool file="emboss/phylipnew/emboss_fneighbor.xml" />
<tool file="emboss/phylipnew/emboss_fprotdist.xml" />
<tool file="emboss/phylipnew/emboss_fprotpars.xml" />
</section> -->
<section name="HYPHY" id="hyphy">
<tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
<tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
</section>
</toolbox>
tool_conf.xml.sample
+22 -207
View File
@@ -3,16 +3,13 @@
<section name="Get Data" id="getext">
<tool file="data_source/upload.xml"/>
<tool file="data_source/ucsc_tablebrowser.xml" />
<tool file="data_source/ucsc_tablebrowser_test.xml" />
<tool file="data_source/ucsc_tablebrowser_archaea.xml" />
<!-- <tool file="data_source/ucsc_proxy.xml"/>
<tool file="data_source/ucsc_testproxy.xml" />
<tool file="data_source/ucsc_archaea.xml" /> -->
<tool file="data_source/ucsc_tablebrowser_test.xml" />
<tool file="data_source/ucsc_archaea.xml" />
<tool file="data_source/microbial_import.xml" />
<tool file="data_source/biomart.xml" />
<tool file="data_source/biomart_test.xml" />
<tool file="data_source/encode_db.xml" />
<tool file="data_source/hbvar.xml" />
<tool file="data_source/hbvar.xml" />
<tool file="validation/fix_errors.xml" />
</section>
<section name="Get ENCODE Data" id="encode">
@@ -24,15 +21,14 @@
<tool file="data_source/encode_import_gencode.xml" />
</section>
<section name="ENCODE Tools" id="EncodeTools">
<tool file="extract/interval2maf.xml" />
<!-- <tool file="extract/interval2maf.xml" />
<tool file="extract/phastOdds/phastOdds_tool.xml" />
<tool file="stats/aggregate_binned_scores_in_intervals.xml" />
<tool file="stats/aggregate_binned_scores_in_intervals.xml" /> -->
<tool file="encode/gencode_partition.xml" />
<tool file="encode/random_intervals.xml" />
</section>
<section name="Edit Queries" id="textutil">
<section name="Text Manipulation" id="textutil">
<tool file="filters/fixedValueColumn.xml" />
<!-- <tool file="operations/combineLists.xml" /> -->
<tool file="stats/column_maker.xml" />
<tool file="filters/catWrapper.xml" />
<tool file="filters/condense_characters.xml" />
@@ -44,20 +40,21 @@
<tool file="filters/headWrapper.xml" />
<tool file="filters/tailWrapper.xml" />
</section>
<section name="Filter, Sort, Join, Compare, Subtract" id="filter">
<tool file="stats/grouping.xml" />
<section name="Filter and Sort" id="filter">
<tool file="stats/filtering.xml" />
<tool file="filters/sorter.xml" />
<tool file="filters/grep.xml" />
</section>
<section name="Join, Subtract and Group" id="group">
<tool file="filters/joiner.xml" />
<tool file="filters/compare.xml"/>
<tool file="new_operations/subtract_query.xml"/>
<tool file="stats/grouping.xml" />
</section>
<section name="Convert Formats" id="convert">
<tool file="filters/maf/maf_to_fasta_multiple_sets.xml" />
<tool file="filters/maf/maf_to_fasta_concat.xml" />
<tool file="filters/maf/maf_to_bed.xml" />
<tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
<tool file="filters/gff2bed.xml" />
<tool file="filters/bed2gff.xml" />
<tool file="filters/axt_to_fasta.xml" />
@@ -65,13 +62,18 @@
<tool file="filters/axt_to_lav.xml" />
<tool file="filters/lav_to_bed.xml" />
</section>
<section name="Extract Features" id="features">
<tool file="filters/ucsc_gene_bed_to_exon_bed.xml" />
<tool file="extract/extract_GFF_Features.xml" />
</section>
<section name="Pattern-Matching" id="patmat">
<tool file="patmat/findcluster_mysql.xml" />
</section>
<section name="Fetch Sequences and Alignments" id="extract">
<section name="Fetch Sequences" id="fetchSeq">
<tool file="extract/fasta-subseq-wrapper.xml" />
<tool file="extract/twoBitToFa_wrapper.xml" />
<tool file="extract/extractAxt_wrapper.xml" />
</section>
<section name="Fetch Alignments" id="fetchAlign">
<tool file="extract/interval2maf_pairwise.xml" />
<tool file="extract/interval2maf.xml" />
<tool file="extract/user_interval2maf.xml" />
@@ -83,9 +85,7 @@
<tool file="filters/maf/maf_limit_to_species.xml"/>
<tool file="filters/maf/maf_limit_size.xml"/>
<tool file="filters/maf/maf_by_block_number.xml"/>
<tool file="extract/extract_GFF_Features.xml" />
</section>
<section name="Get Genomic Scores" id="scores">
<tool file="stats/wiggle_to_simple.xml" />
<tool file="stats/aggregate_binned_scores_in_intervals.xml" />
@@ -117,6 +117,11 @@
<tool file="data_source/show_in_ucsc.xml" />
<tool file="visualization/build_ucsc_custom_track.xml" />
</section>
<section name="Evolution: HyPhy" id="hyphy">
<tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
<tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
<tool file="hyphy/hyphy_dnds_wrapper.xml" />
</section>
<section name="EMBOSS" id="EMBOSSLite">
<tool file="emboss/emboss_cai.xml" />
<tool file="emboss/emboss_cai_custom.xml" />
@@ -174,194 +179,4 @@
<tool file="emboss/emboss_charge.xml" />
<tool file="emboss/emboss_checktrans.xml" />
</section>
<!--
<section name="Run EMBOSS nucleotide" id="EMBOSSnucleotide">
<tool file="emboss/emboss_biosed.xml" />
<tool file="emboss/emboss_btwisted.xml" />
<tool file="emboss/emboss_cai.xml" />
<tool file="emboss/emboss_chaos.xml" />
<tool file="emboss/emboss_chips.xml" />
<tool file="emboss/emboss_codcmp.xml" />
<tool file="emboss/emboss_coderet.xml" />
<tool file="emboss/emboss_compseq.xml" />
<tool file="emboss/emboss_cpgplot.xml" />
<tool file="emboss/emboss_cpgreport.xml" />
<tool file="emboss/emboss_cusp.xml" />
<tool file="emboss/emboss_cutseq.xml" />
<tool file="emboss/emboss_dan.xml" />
<tool file="emboss/emboss_degapseq.xml" />
<tool file="emboss/emboss_descseq.xml" />
<tool file="emboss/emboss_diffseq.xml" />
<tool file="emboss/emboss_dotmatcher.xml" />
<tool file="emboss/emboss_dotpath.xml" />
<tool file="emboss/emboss_dottup.xml" />
<tool file="emboss/emboss_einverted.xml" />
<tool file="emboss/emboss_equicktandem.xml" />
<tool file="emboss/emboss_est2genome.xml" />
<tool file="emboss/emboss_etandem.xml" />
<tool file="emboss/emboss_extractfeat.xml" />
<tool file="emboss/emboss_extractseq.xml" />
<tool file="emboss/emboss_freak.xml" />
<tool file="emboss/emboss_fuzznuc.xml" />
<tool file="emboss/emboss_fuzztran.xml" />
<tool file="emboss/emboss_geecee.xml" />
<tool file="emboss/emboss_getorf.xml" />
<tool file="emboss/emboss_helixturnhelix.xml" />
<tool file="emboss/emboss_infoseq.xml" />
<tool file="emboss/emboss_isochore.xml" />
<tool file="emboss/emboss_marscan.xml" />
<tool file="emboss/emboss_maskfeat.xml" />
<tool file="emboss/emboss_maskseq.xml" />
<tool file="emboss/emboss_matcher.xml" />
<tool file="emboss/emboss_megamerger.xml" />
<tool file="emboss/emboss_merger.xml" />
<tool file="emboss/emboss_msbar.xml" />
<tool file="emboss/emboss_needle.xml" />
<tool file="emboss/emboss_newcpgreport.xml" />
<tool file="emboss/emboss_newcpgseek.xml" />
<tool file="emboss/emboss_newseq.xml" />
<tool file="emboss/emboss_noreturn.xml" />
<tool file="emboss/emboss_notseq.xml" />
<tool file="emboss/emboss_nthseq.xml" />
<tool file="emboss/emboss_palindrome.xml" />
<tool file="emboss/emboss_pasteseq.xml" />
<tool file="emboss/emboss_plotorf.xml" />
<tool file="emboss/emboss_polydot.xml" />
<tool file="emboss/emboss_prettyseq.xml" />
<tool file="emboss/emboss_primersearch.xml" />
<tool file="emboss/emboss_revseq.xml" />
<tool file="emboss/emboss_seqmatchall.xml" />
<tool file="emboss/emboss_seqret.xml" />
<tool file="emboss/emboss_showfeat.xml" />
<tool file="emboss/emboss_showorf.xml" />
<tool file="emboss/emboss_shuffleseq.xml" />
<tool file="emboss/emboss_sirna.xml" />
<tool file="emboss/emboss_sixpack.xml" />
<tool file="emboss/emboss_skipseq.xml" />
<tool file="emboss/emboss_splitter.xml" />
<tool file="emboss/emboss_stretcher.xml" />
<tool file="emboss/emboss_stssearch.xml" />
<tool file="emboss/emboss_supermatcher.xml" />
<tool file="emboss/emboss_syco.xml" />
<tool file="emboss/emboss_tcode.xml" />
<tool file="emboss/emboss_textsearch.xml" />
<tool file="emboss/emboss_tranalign.xml" />
<tool file="emboss/emboss_transeq.xml" />
<tool file="emboss/emboss_trimest.xml" />
<tool file="emboss/emboss_trimseq.xml" />
<tool file="emboss/emboss_twofeat.xml" />
<tool file="emboss/emboss_union.xml" />
<tool file="emboss/emboss_vectorstrip.xml" />
<tool file="emboss/emboss_water.xml" />
<tool file="emboss/emboss_wobble.xml" />
<tool file="emboss/emboss_wordcount.xml" />
<tool file="emboss/emboss_wordmatch.xml" />
</section>
<section name="Run EMBOSS protein" id="EMBOSSprotein">
<tool file="emboss/emboss_antigenic.xml" />
<tool file="emboss/emboss_backtranseq.xml" />
<tool file="emboss/emboss_biosed.xml" />
<tool file="emboss/emboss_chaos.xml" />
<tool file="emboss/emboss_charge.xml" />
<tool file="emboss/emboss_checktrans.xml" />
<tool file="emboss/emboss_coderet.xml" />
<tool file="emboss/emboss_compseq.xml" />
<tool file="emboss/emboss_cutseq.xml" />
<tool file="emboss/emboss_degapseq.xml" />
<tool file="emboss/emboss_descseq.xml" />
<tool file="emboss/emboss_diffseq.xml" />
<tool file="emboss/emboss_digest.xml" />
<tool file="emboss/emboss_dotmatcher.xml" />
<tool file="emboss/emboss_dotpath.xml" />
<tool file="emboss/emboss_dottup.xml" />
<tool file="emboss/emboss_epestfind.xml" />
<tool file="emboss/emboss_extractfeat.xml" />
<tool file="emboss/emboss_extractseq.xml" />
<tool file="emboss/emboss_freak.xml" />
<tool file="emboss/emboss_fuzzpro.xml" />
<tool file="emboss/emboss_garnier.xml" />
<tool file="emboss/emboss_hmoment.xml" />
<tool file="emboss/emboss_iep.xml" />
<tool file="emboss/emboss_infoseq.xml" />
<tool file="emboss/emboss_maskfeat.xml" />
<tool file="emboss/emboss_maskseq.xml" />
<tool file="emboss/emboss_matcher.xml" />
<tool file="emboss/emboss_msbar.xml" />
<tool file="emboss/emboss_needle.xml" />
<tool file="emboss/emboss_newseq.xml" />
<tool file="emboss/emboss_noreturn.xml" />
<tool file="emboss/emboss_notseq.xml" />
<tool file="emboss/emboss_nthseq.xml" />
<tool file="emboss/emboss_octanol.xml" />
<tool file="emboss/emboss_oddcomp.xml" />
<tool file="emboss/emboss_pasteseq.xml" />
<tool file="emboss/emboss_patmatdb.xml" />
<tool file="emboss/emboss_pepcoil.xml" />
<tool file="emboss/emboss_pepinfo.xml" />
<tool file="emboss/emboss_pepstats.xml" />
<tool file="emboss/emboss_pepwheel.xml" />
<tool file="emboss/emboss_pepwindow.xml" />
<tool file="emboss/emboss_pepwindowall.xml" />
<tool file="emboss/emboss_polydot.xml" />
<tool file="emboss/emboss_seqmatchall.xml" />
<tool file="emboss/emboss_seqret.xml" />
<tool file="emboss/emboss_showfeat.xml" />
<tool file="emboss/emboss_shuffleseq.xml" />
<tool file="emboss/emboss_sigcleave.xml" />
<tool file="emboss/emboss_skipseq.xml" />
<tool file="emboss/emboss_splitter.xml" />
<tool file="emboss/emboss_stretcher.xml" />
<tool file="emboss/emboss_supermatcher.xml" />
<tool file="emboss/emboss_textsearch.xml" />
<tool file="emboss/emboss_tmap.xml" />
<tool file="emboss/emboss_tranalign.xml" />
<tool file="emboss/emboss_trimseq.xml" />
<tool file="emboss/emboss_twofeat.xml" />
<tool file="emboss/emboss_union.xml" />
<tool file="emboss/emboss_water.xml" />
<tool file="emboss/emboss_wordmatch.xml" />
</section>
-->
<!--
<section id="ePHYLIP" name="Run ePHYLIP">
<tool file="emboss/phylip/emboss_eclique.xml" />
<tool file="emboss/phylip/emboss_econsense.xml" />
<tool file="emboss/phylip/emboss_econtml.xml" />
<tool file="emboss/phylip/emboss_econtrast.xml" />
<tool file="emboss/phylip/emboss_ednacomp.xml" />
<tool file="emboss/phylip/emboss_ednadist.xml" />
<tool file="emboss/phylip/emboss_ednainvar.xml" />
<tool file="emboss/phylip/emboss_ednaml.xml" />
<tool file="emboss/phylip/emboss_ednamlk.xml" />
<tool file="emboss/phylip/emboss_ednapars.xml" />
<tool file="emboss/phylip/emboss_ednapenny.xml" />
<tool file="emboss/phylip/emboss_edollop.xml" />
<tool file="emboss/phylip/emboss_edolpenny.xml" />
<tool file="emboss/phylip/emboss_efactor.xml" />
<tool file="emboss/phylip/emboss_efitch.xml" />
<tool file="emboss/phylip/emboss_egendist.xml" />
<tool file="emboss/phylip/emboss_ekitsch.xml" />
<tool file="emboss/phylip/emboss_emix.xml" />
<tool file="emboss/phylip/emboss_eneighbor.xml" />
<tool file="emboss/phylip/emboss_epenny.xml" />
<tool file="emboss/phylip/emboss_eprotdist.xml" />
<tool file="emboss/phylip/emboss_eprotpars.xml" />
<tool file="emboss/phylip/emboss_erestml.xml" />
<tool file="emboss/phylip/emboss_eseqboot.xml" />
</section>
-->
<section name="PHYLIP" id="phylipnew">
<tool file="emboss/phylipnew/emboss_fdnadist.xml" />
<tool file="emboss/phylipnew/emboss_fdnapars.xml" />
<tool file="emboss/phylipnew/emboss_fdrawgram.xml" />
<tool file="emboss/phylipnew/emboss_ffitch.xml" />
<tool file="emboss/phylipnew/emboss_fseqboot.xml" />
<tool file="emboss/phylipnew/emboss_fneighbor.xml" />
<tool file="emboss/phylipnew/emboss_fprotdist.xml" />
<tool file="emboss/phylipnew/emboss_fprotpars.xml" />
</section>
<section name="HYPHY" id="hyphy">
<tool file="hyphy/hyphy_branch_lengths_wrapper.xml" />
<tool file="hyphy/hyphy_nj_tree_wrapper.xml" />
</section>
</toolbox>
tools/extract/fasta-subseq-wrapper.xml
+16 -14
View File
@@ -1,5 +1,5 @@
<tool id="Extract genomic DNA 1" name="Extract genomic DNA">
<description>corresponding to query coordinates</description>
<description>using coordinates from assembled genomes</description>
<command interpreter="perl">fasta-subseq-wrapper.pl -i $input -o $out_file1 -p $input_chromCol $input_startCol $input_endCol $input_strandCol -g $dbkey</command>
<inputs>
<param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query"/>
@@ -19,30 +19,32 @@
Make sure that the genome build is specified for the interval dataset you are extracting sequences for (click the pencil icon if it is not specified). However, if the build is specified and the tool still gives you an error, your genome of interest may only be partially assembled (ie, in scaffolds). To extract sequences from such partially assembled genomes use *Extract Genomic DNA from unassmebled genomes* tool.
.. class:: infomark
Why do we have two sequence extractors?
* **Extract genomic DNA using coordinates from ASSEMBLED genomes** (this tool) - will work for most cases when your intervals are located on assembled chromosomes (i.e., chr1, chrX, etc.)
* **Extract genomic DNA using coordinates from UNassembled genomes** - is designed to work on partially assembled or unassembled genomes when your intervals are located in contigs or scaffolds rather than assembled chromosomes (i.e., super_1 etc.)
These two tools will be merged in the future.
-----
**Syntax**
**What it does**
This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA format.
- **FASTA format** a text-based format for representing both nucleic and protein sequences, in which base pairs or proteins are represented using a single-letter code.
- This format contains a one line header. It starts with a " >" symbol. The first word on this line is the name of the sequence. The rest of the line is a description of the sequence.
- The remaining lines contain the sequence itself.
- Blank lines in a FASTA file are ignored, and so are spaces or other gap symbols (dashes, underscores, periods) in a sequence.
- Fasta files containing multiple sequences are just the same, with one sequence listed right after another. This format is accepted for many multiple sequence alignment programs.
-----
**Example**
- Input dataset::
Input dataset::
chr7 127475281 127475310 NM_000230 0 +
chr7 127485994 127486166 NM_000230 0 +
chr7 127486011 127486166 D49487 0 +
chr7 127475281 127475310 NM_000230 0 +
chr7 127485994 127486166 NM_000230 0 +
chr7 127486011 127486166 D49487 0 +
- Fetch genomic DNAs of the above data::
Fetch genomic DNAs of the above data::
&gt;hg17_chr7_127475281_127475310_+
GTAGGAATCGCAGCGCCAGCGGTTGCAAG
tools/extract/twoBitToFa_wrapper.xml
+18 -16
View File
@@ -1,5 +1,5 @@
<tool id="Extract genomic DNA2" name="Extract genomic DNA">
<description>from unassembled genome coordinates</description>
<description>using coordinates from UNassembled genomes</description>
<command interpreter="perl">twoBitToFa_wrapper.py $input $out_file1 $input_chromCol $input_startCol $input_endCol $input_strandCol $dbkey "/depot/data2/galaxy/twobit.loc"</command>
<inputs>
<param format="interval" name="input" type="data" label="Fetch sequences corresponding to Query"/>
@@ -17,32 +17,34 @@
.. class:: warningmark
Make sure the input data has been specified a database build.
Make sure that the genome build is specified for the interval dataset you are extracting sequences for (click the pencil icon if it is not specified).
.. class:: infomark
Why do we have two sequence extractors?
* **Extract genomic DNA using coordinates from ASSEMBLED genomes** - will work for most cases when your intervals are located on assembled chromosomes (i.e., chr1, chrX, etc.)
* **Extract genomic DNA using coordinates from UNassembled genomes** (this tool) - is designed to work on partially assembled or unassembled genomes when your intervals are located in contigs or scaffolds rather than assembled chromosomes (i.e., super_1 etc.)
These two tools will be merged in the future.
-----
**Syntax**
**What it does**
This tool uses coordinate, strand, and build information to fetch genomic DNAs from partially assembled and unassembled genomes in FASTA format.
- **FASTA format** a text-based format for representing both nucleic and protein sequences, in which base pairs or proteins are represented using a single-letter code.
- This format contains a one line header. It starts with a " >" symbol. The first word on this line is the name of the sequence. The rest of the line is a description of the sequence.
- The remaining lines contain the sequence itself.
- Blank lines in a FASTA file are ignored, and so are spaces or other gap symbols (dashes, underscores, periods) in a sequence.
- Fasta files containing multiple sequences are just the same, with one sequence listed right after another. This format is accepted for many multiple sequence alignment programs.
This tool uses coordinate, strand, and build information to fetch genomic DNAs in FASTA format.
-----
**Example**
- Input dataset::
Input dataset::
super_1 127475281 127475310 NM_000230 0 +
super_1 127485994 127486166 NM_000230 0 +
super_1 127486011 127486166 D49487 0 +
super_1 127475281 127475310 NM_000230 0 +
super_1 127485994 127486166 NM_000230 0 +
super_1 127486011 127486166 D49487 0 +
- Fetch genomic DNAs of the above data::
Fetch genomic DNAs of the above data::
&gt;super_1:127475281-127475310
GTAGGAATCGCAGCGCCAGCGGTTGCAAG
tools/plotting/xy_plot.xml
+2 -2
View File
@@ -1,5 +1,5 @@
<tool id="XY_Plot_1" name="XY Plot">
<description> of two numeric columns</description>
<tool id="XY_Plot_1" name="Plotting tool">
<description>for multiple series and graph types</description>
<command interpreter="bash">r_wrapper.sh $script_file</command>
<inputs>