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diff test-data/gff3/test.xml @ 17:ff11d442feed draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
author iuc
date Wed, 15 Nov 2017 15:15:27 -0500
parents ad4b9d7eae6a
children 1cfc579079a6
line wrap: on
line diff
--- a/test-data/gff3/test.xml	Wed Sep 13 13:07:20 2017 -0400
+++ b/test-data/gff3/test.xml	Wed Nov 15 15:15:27 2017 -0500
@@ -3,7 +3,27 @@
     <metadata>
         <gencode>11</gencode>
         <genomes>
-                  <genome>test-data/merlin.fa</genome>
+                  <genome path="/tmp/tmpnh6QWY/files/000/dataset_5.dat">
+                    <metadata>
+                      <dataset id="7b55dbb89df8f4e5" hid="1"
+                          size="171.6 KB"
+                          edam_format="format_1929"
+                          file_ext="fasta" />
+                      <history id="54f2a3a23292eb07"
+                          user_email="test@bx.psu.edu"
+                          user_id="2"
+                          display_name="test_history"/>
+                      <metadata
+                          dbkey="hg17"
+                          data_lines="2881"
+                          sequences="1"
+                          />
+                      <tool
+                          tool_id="upload1"
+                          tool_version="1.1.4"
+                          />
+                    </metadata>
+                  </genome>
         </genomes>
         <general>
             <defaultLocation></defaultLocation>
@@ -17,22 +37,122 @@
             <show_menu>true</show_menu>
             <hideGenomeOptions>false</hideGenomeOptions>
         </general>
+        <galaxyUrl>http://localhost:8080</galaxyUrl>
     </metadata>
     <tracks>
         <track cat="Auto Coloured" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="A"/>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="B"/>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="C"/>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="D"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_6.dat" ext="gff3" label="A.gff">
+                <metadata>
+                  <dataset id="fa6d20d0fb68383f" hid="2"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="hg17"
+                      data_lines="27"
+                      comment_lines="19"
+                      columns="9"
+                      column_names=""
+                      delimiter="__tc__"
+                      attributes="6"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.4"
+                      />
+                </metadata>
+              </trackFile>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_7.dat" ext="gff3" label="B.gff">
+                <metadata>
+                  <dataset id="683bc220e21425bb" hid="3"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="hg17"
+                      data_lines="27"
+                      comment_lines="19"
+                      columns="9"
+                      column_names=""
+                      delimiter="__tc__"
+                      attributes="6"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.4"
+                      />
+                </metadata>
+              </trackFile>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_8.dat" ext="gff3" label="C.gff">
+                <metadata>
+                  <dataset id="a90a30fafe298e1e" hid="4"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="hg17"
+                      data_lines="27"
+                      comment_lines="19"
+                      columns="9"
+                      column_names=""
+                      delimiter="__tc__"
+                      attributes="6"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.4"
+                      />
+                </metadata>
+              </trackFile>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_9.dat" ext="gff3" label="D.gff">
+                <metadata>
+                  <dataset id="b842d972534ccb3e" hid="5"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="hg17"
+                      data_lines="27"
+                      comment_lines="19"
+                      columns="9"
+                      column_names=""
+                      delimiter="__tc__"
+                      attributes="6"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.4"
+                      />
+                </metadata>
+              </trackFile>
             </files>
 
             <options>
                 <style>
+                    <overridePlugins>False</overridePlugins>
+                    <overrideDraggable>False</overrideDraggable>
                     <className>feature</className>
                     <description>note,description</description>
-                    <label>name,id</label>
-                    <height>100px</height>
+                    <label>product,name,id</label>
+                    <height>10px</height>
+                    <maxHeight>600</maxHeight>
                 </style>
                 <scaling>
                         <method>ignore</method>
@@ -51,15 +171,42 @@
         </track>
         <track cat="Ignore Scale" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Fixed Colour"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+                <metadata>
+                  <dataset id="5449172d6ff5669b" hid="6"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="hg17"
+                      data_lines="27"
+                      comment_lines="19"
+                      columns="9"
+                      column_names=""
+                      delimiter="__tc__"
+                      attributes="6"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.4"
+                      />
+                </metadata>
+              </trackFile>
             </files>
 
             <options>
                 <style>
+                    <overridePlugins>False</overridePlugins>
+                    <overrideDraggable>False</overrideDraggable>
                     <className>feature</className>
                     <description>note,description</description>
-                    <label>name,id</label>
-                    <height>100px</height>
+                    <label>product,name,id</label>
+                    <height>10px</height>
+                    <maxHeight>600</maxHeight>
                 </style>
                 <scaling>
                         <method>ignore</method>
@@ -78,15 +225,42 @@
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+                <metadata>
+                  <dataset id="5449172d6ff5669b" hid="6"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="hg17"
+                      data_lines="27"
+                      comment_lines="19"
+                      columns="9"
+                      column_names=""
+                      delimiter="__tc__"
+                      attributes="6"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.4"
+                      />
+                </metadata>
+              </trackFile>
             </files>
 
             <options>
                 <style>
+                    <overridePlugins>False</overridePlugins>
+                    <overrideDraggable>False</overrideDraggable>
                     <className>feature</className>
                     <description>note,description</description>
-                    <label>name,id</label>
-                    <height>100px</height>
+                    <label>product,name,id</label>
+                    <height>10px</height>
+                    <maxHeight>600</maxHeight>
                 </style>
                 <scaling>
                         <method>score</method>
@@ -111,15 +285,42 @@
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Auto-bounds, Fixed Color"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+                <metadata>
+                  <dataset id="5449172d6ff5669b" hid="6"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="hg17"
+                      data_lines="27"
+                      comment_lines="19"
+                      columns="9"
+                      column_names=""
+                      delimiter="__tc__"
+                      attributes="6"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.4"
+                      />
+                </metadata>
+              </trackFile>
             </files>
 
             <options>
                 <style>
+                    <overridePlugins>False</overridePlugins>
+                    <overrideDraggable>False</overrideDraggable>
                     <className>feature</className>
                     <description>note,description</description>
-                    <label>name,id</label>
-                    <height>100px</height>
+                    <label>product,name,id</label>
+                    <height>10px</height>
+                    <maxHeight>600</maxHeight>
                 </style>
                 <scaling>
                         <method>score</method>
@@ -144,15 +345,42 @@
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+                <metadata>
+                  <dataset id="5449172d6ff5669b" hid="6"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="hg17"
+                      data_lines="27"
+                      comment_lines="19"
+                      columns="9"
+                      column_names=""
+                      delimiter="__tc__"
+                      attributes="6"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.4"
+                      />
+                </metadata>
+              </trackFile>
             </files>
 
             <options>
                 <style>
+                    <overridePlugins>False</overridePlugins>
+                    <overrideDraggable>False</overrideDraggable>
                     <className>feature</className>
                     <description>note,description</description>
-                    <label>name,id</label>
-                    <height>100px</height>
+                    <label>product,name,id</label>
+                    <height>10px</height>
+                    <maxHeight>600</maxHeight>
                 </style>
                 <scaling>
                         <method>score</method>
@@ -179,15 +407,42 @@
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/1.gff" ext="gff3" label="Linear, Manual Bounds, Fixed Color"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+                <metadata>
+                  <dataset id="5449172d6ff5669b" hid="6"
+                      size="2.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="hg17"
+                      data_lines="27"
+                      comment_lines="19"
+                      columns="9"
+                      column_names=""
+                      delimiter="__tc__"
+                      attributes="6"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.4"
+                      />
+                </metadata>
+              </trackFile>
             </files>
 
             <options>
                 <style>
+                    <overridePlugins>False</overridePlugins>
+                    <overrideDraggable>False</overrideDraggable>
                     <className>feature</className>
                     <description>note,description</description>
-                    <label>name,id</label>
-                    <height>100px</height>
+                    <label>product,name,id</label>
+                    <height>10px</height>
+                    <maxHeight>600</maxHeight>
                 </style>
                 <scaling>
                         <method>score</method>
@@ -214,15 +469,42 @@
         </track>
         <track cat="Realistic" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/interpro.gff" ext="gff3" label="Interpro data"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_11.dat" ext="gff3" label="interpro.gff">
+                <metadata>
+                  <dataset id="9ce08b2254e4d5ed" hid="7"
+                      size="103.3 KB"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="hg17"
+                      data_lines="556"
+                      comment_lines="2"
+                      columns="9"
+                      column_names=""
+                      delimiter="__tc__"
+                      attributes="11"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.4"
+                      />
+                </metadata>
+              </trackFile>
             </files>
 
             <options>
                 <style>
+                    <overridePlugins>False</overridePlugins>
+                    <overrideDraggable>False</overrideDraggable>
                     <className>feature</className>
                     <description>note,description</description>
-                    <label>name,id</label>
-                    <height>100px</height>
+                    <label>product,name,id</label>
+                    <height>10px</height>
+                    <maxHeight>600</maxHeight>
                 </style>
                 <scaling>
                         <method>ignore</method>
@@ -241,15 +523,42 @@
         </track>
         <track cat="Realistic" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="test-data/gff3/2.gff" ext="gff3" label="Match/Match Part"/>
+              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_12.dat" ext="gff3" label="2.gff">
+                <metadata>
+                  <dataset id="80b8022ff3f677b7" hid="8"
+                      size="326 bytes"
+                      edam_format="format_1975"
+                      file_ext="gff3" />
+                  <history id="54f2a3a23292eb07"
+                      user_email="test@bx.psu.edu"
+                      user_id="2"
+                      display_name="test_history"/>
+                  <metadata
+                      dbkey="hg17"
+                      data_lines="3"
+                      comment_lines="3"
+                      columns="9"
+                      column_names=""
+                      delimiter="__tc__"
+                      attributes="4"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.4"
+                      />
+                </metadata>
+              </trackFile>
             </files>
 
             <options>
                 <style>
+                    <overridePlugins>False</overridePlugins>
+                    <overrideDraggable>False</overrideDraggable>
                     <className>feature</className>
                     <description>note,description</description>
-                    <label>name,id</label>
-                    <height>100px</height>
+                    <label>product,name,id</label>
+                    <height>10px</height>
+                    <maxHeight>600</maxHeight>
                 </style>
                 <scaling>
                         <method>ignore</method>
@@ -268,4 +577,10 @@
             </options>
         </track>
     </tracks>
+    <plugins
+        ComboTrackSelector=""
+        Bookmarks=""
+        GCContent=""
+        theme=""
+        />
 </root>