[galaxy-dev] listing the same tool twice in tool_conf.xml
Hi All, My group is trying to create some custom sections in the Tools pane, and have run into an issue. We have a custom section, within which there are three different labels and several tools under each label. We are trying list the same tool under two different labels within the same section. However, the second occurrence of the tool is not displayed. Is it possible to list the same tool twice under the same section? -- Branden Timm bt...@glbrc.wisc.edu ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] listing the same tool twice in tool_conf.xml
On 02/21/2011 04:05 PM, Branden Timm wrote: Hi All, My group is trying to create some custom sections in the Tools pane, and have run into an issue. We have a custom section, within which there are three different labels and several tools under each label. We are trying list the same tool under two different labels within the same section. However, the second occurrence of the tool is not displayed. Is it possible to list the same tool twice under the same section? Hi Brandon make a copy of the tool definition xml file and change the value for 'id' in the first line and then refer to the copy in the tool_conf.xml file for the second occurrence .that should do the trick. Regards, Hans Branden Timm bt...@glbrc.wisc.edu ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] listing the same tool twice in tool_conf.xml
Branden, we have also customised the tol menu and added a university specific section on top just beneath Get data. We have also listed tools twice for convenience. I do not see the need t list a tool twice in the same expanding section. But in another section it should work flawlessly. Having duplicate XML configs can be an issue in future mainetnance. Below a snippet of our tool config. For instance in this (snipped) piece the BLAT_synteny_tool is listed twice in section Artemis. label Artemis... but also insection local BLAT. Alex ?xml version=1.0? toolbox section name=Get Data id=getext tool file=data_source/upload.xml/ tool file=data_source/microbial_import.xml / snip /section section name=Get from web id=webget tool file=data_source/ucsc_tablebrowser.xml / tool file=data_source/ucsc_tablebrowser_test.xml / snip tool file=data_source/epigraph_import.xml / tool file=data_source/epigraph_import_test.xml / tool file=data_source/hbvar.xml / tool file=validation/fix_errors.xml / /section label text=WUR tools id=wur_tools / section name=Artemis/MUMmer id=Artemis_MUMmer_tools tool file=WURtools/genomview_03.xml / label text=MUMmer tools id=MUMmertools / tool file=WURtools/MUMmer/mummer_tool.xml / tool file=WURtools/MUMmer/run_multi_mummer.xml / tool file=WURtools/MUMmer/mummer_maxmatch.xml / tool file=WURtools/MUMmer/mummer_clustering.xml / tool file=WURtools/MUMmer/mummer_utilities_tool.xml / tool file=WURtools/MUMmer/mummerplot_tool.xml / label text=Artemis tools id=Artemistools / tool file=WURtools/BLAT_synteny_tool.xml / tool file=WURtools/JoinContigs_galaxy.xml / tool file=WURtools/JoinCoverage_galaxy.xml / tool file=WURtools/genoPlot_03.xml / tool file=WURtools/Artemis/nucmer_coords2ACT_galaxy.xml / snip /section section name=Local BLAT/BLAST id=BLATBLAST_tools tool file=WURtools/blat_tool.xml/ tool file=WURtools/BLAT_synteny_tool.xml / tool file=WURtools/blastxml_to_eXtra_tabular.xml / tool file=WURtools/blastdbcmd.xml / label text=NCBI BLAST+ id=ncbi_blast_plus_tools / tool file=ncbi_blast_plus/ncbi_blastn_wrapper.xml / snip the rest Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] namens Branden Timm [bt...@wisc.edu] Verzonden: maandag 21 februari 2011 16:05 Aan: galaxy-...@bx.psu.edu Onderwerp: [galaxy-dev] listing the same tool twice in tool_conf.xml Hi All, My group is trying to create some custom sections in the Tools pane, and have run into an issue. We have a custom section, within which there are three different labels and several tools under each label. We are trying list the same tool under two different labels within the same section. However, the second occurrence of the tool is not displayed. Is it possible to list the same tool twice under the same section? -- Branden Timm bt...@glbrc.wisc.edu ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
