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
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