annotate idpicker.xml @ 14:ba68d2bdf5df draft

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<tool id="idpicker" name="IDPicker 3" version="0.1.0-alpha">
  <description>
    Assemble parsimonious protien identifications.
  </description>
  <configfiles>
    <configfile name="group_config"># Simple format group:group_name followed by pairs of name:name and path:path lines
#for $group in $groups:
group:$group.group_name
#for $idpdb_input in $group.idpdb_inputs:
name:${idpdb_input.display_name}
path:${idpdb_input}
#end for
#end for
    </configfile>
  </configfiles>
  <command interpreter="python">
    idpicker_wrapper.py --input $group_config --output $output
  </command>
  <inputs>
    <param format="idpdb" name="outside_inputs" type="data" multiple="true" label="idpDB Inputs" help="Run results through idpQonvert tool to produce idpDB files for IDPicker." />
    <repeat name="groups" title="Experimental Group">
      <param name="group_name" type="text" label="Group Name" help="Name for the group (use only letters and numbers)." />
      <param format="idpdb" name="idpdb_inputs" type="data" multiple="true" label="idpDB Inputs" help="Run results through idpQonvert tool to produce idpDB files for IDPicker." />
    </repeat>
  </inputs>
  <outputs>
    <data format="idpdb" name="output" />
  </outputs>
  <requirements>
    <requirement type="package">idpicker</requirement>
  </requirements>
  <help>
**WARNING**

This tool does not current work.

**What it does**



** Building Groups **

Build arbitrary hierarchy by nesting groups with colon (e.g. control:666Gx6).

http://fenchurch.mc.vanderbilt.edu/bumbershoot/idpicker/index_files/image003.gif

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**Citation**

For the underlying tool, please cite `TODO`

If you use this tool in Galaxy, please cite TODO
  </help>
</tool>