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/protvis_mzml.xml

Created December 18, 2012 22:06
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Example display application using app parameters. Notice the new allow_override="True" on params peptide and spectrum.
Raw
protvis_mzml.xml
<display id="protvis_mzml" version="1.0.0" name="display with ProtVis">
<dynamic_links from_file="tool-data/protk_display_site.txt" skip_startswith="#" id="0" name="0">
<!-- Define parameters by column from file -->
<dynamic_param name="site_id" value="0"/>
<dynamic_param name="site_url" value="1"/>
<!-- We define url and params as normal, but values defined in dynamic_param are available by specified name -->
<url target_frame="galaxy_main">${site_url}/init_url?url=${mzml_file.qp}&amp;type=mzml${peptide_param.value}${spectrum_param.value}</url>
<param type="data" name="mzml_file" url="galaxy_${DATASET_HASH}.mzml" />
<param type="template" name="peptide" allow_override="True" />
<param type="template" name="peptide_param" strip="True">
#if str($peptide)
&amp;peptide=$qp($peptide)
#end if
</param>
<param type="template" name="spectrum" allow_override="True" />
<param type="template" name="spectrum_param" strip="True">
#if str($spectrum)
&amp;scan=$qp($spectrum)
#end if
</param>
</dynamic_links>
</display>
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