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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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1 <tool name="Graph Viewer" id="graph_viewer" tool_type="data_source">
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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2 <description></description>
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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3 <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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4 <inputs action="http://localhost/viewer/index.html" check_values="false" method="get">
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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5 <display>go to Graph Viewer $GALAXY_URL</display>
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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6 <param name="GALAXY_URL" type="baseurl" value="/tool_runner" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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7 <param name="tool_id" type="hidden" value="ucsc_table_direct1" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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8 <param name="sendToGalaxy" type="hidden" value="1" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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9 <param name="hgta_compressType" type="hidden" value="none" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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10 <param name="hgta_outputType" type="hidden" value="bed" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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11 </inputs>
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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12 <request_param_translation>
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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13 <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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14 <request_param galaxy_name="URL" remote_name="URL" missing="" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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15 <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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16 <request_param galaxy_name="organism" remote_name="org" missing="unknown species" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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17 <request_param galaxy_name="table" remote_name="hgta_table" missing="unknown table" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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18 <request_param galaxy_name="description" remote_name="hgta_regionType" missing="no description" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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19 <request_param galaxy_name="data_type" remote_name="hgta_outputType" missing="auto" >
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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20 <value_translation>
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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21 <value galaxy_value="auto" remote_value="primaryTable" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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22 <value galaxy_value="auto" remote_value="selectedFields" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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23 <value galaxy_value="wig" remote_value="wigData" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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24 <value galaxy_value="interval" remote_value="tab" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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25 <value galaxy_value="html" remote_value="hyperlinks" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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26 <value galaxy_value="fasta" remote_value="sequence" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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27 <value galaxy_value="gtf" remote_value="gff" />
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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28 </value_translation>
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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29 </request_param>
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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30 </request_param_translation>
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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31 <uihints minwidth="800"/>
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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32 <outputs>
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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33 <data name="output" format="tabular" label="${tool.name} on ${organism}: ${table} (#if $description == 'range' then $getVar( 'position', 'unknown position' ) else $description#)"/>
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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34 </outputs>
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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35 <options sanitize="False" refresh="True"/>
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ryo_tas <yamanaka@genome.rcast.u-tokyo.ac.jp>
parents:
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36 </tool>
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