Mercurial > repos > iuc > jbrowse

diff test-data/gff3/test.xml @ 25:1cfc579079a6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
author iuc
date Tue, 29 Jan 2019 05:34:16 -0500
parents ff11d442feed
children 112eb40ba6cf
line wrap: on
line diff
--- a/test-data/gff3/test.xml	Wed Jan 16 03:28:29 2019 -0500
+++ b/test-data/gff3/test.xml	Tue Jan 29 05:34:16 2019 -0500
@@ -3,27 +3,27 @@
     <metadata>
         <gencode>11</gencode>
         <genomes>
-                  <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>
+              <genome path="/tmp/tmpWtvfKr/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="?"
+                      data_lines="2881"
+                      sequences="1"
+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.6"
+                      />
+                </metadata>
+              </genome>
         </genomes>
         <general>
             <defaultLocation></defaultLocation>
@@ -37,12 +37,12 @@
             <show_menu>true</show_menu>
             <hideGenomeOptions>false</hideGenomeOptions>
         </general>
-        <galaxyUrl>http://localhost:8080</galaxyUrl>
+        <galaxyUrl>http://localhost</galaxyUrl>
     </metadata>
     <tracks>
         <track cat="Auto Coloured" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_6.dat" ext="gff3" label="A.gff">
+              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_6.dat" ext="gff3" label="A.gff">
                 <metadata>
                   <dataset id="fa6d20d0fb68383f" hid="2"
                       size="2.3 KB"
@@ -53,7 +53,7 @@
                       user_id="2"
                       display_name="test_history"/>
                   <metadata
-                      dbkey="hg17"
+                      dbkey="?"
                       data_lines="27"
                       comment_lines="19"
                       columns="9"
@@ -63,11 +63,11 @@
                       />
                   <tool
                       tool_id="upload1"
-                      tool_version="1.1.4"
+                      tool_version="1.1.6"
                       />
                 </metadata>
               </trackFile>
-              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_7.dat" ext="gff3" label="B.gff">
+              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_7.dat" ext="gff3" label="B.gff">
                 <metadata>
                   <dataset id="683bc220e21425bb" hid="3"
                       size="2.3 KB"
@@ -78,7 +78,7 @@
                       user_id="2"
                       display_name="test_history"/>
                   <metadata
-                      dbkey="hg17"
+                      dbkey="?"
                       data_lines="27"
                       comment_lines="19"
                       columns="9"
@@ -88,11 +88,11 @@
                       />
                   <tool
                       tool_id="upload1"
-                      tool_version="1.1.4"
+                      tool_version="1.1.6"
                       />
                 </metadata>
               </trackFile>
-              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_8.dat" ext="gff3" label="C.gff">
+              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_8.dat" ext="gff3" label="C.gff">
                 <metadata>
                   <dataset id="a90a30fafe298e1e" hid="4"
                       size="2.3 KB"
@@ -103,7 +103,7 @@
                       user_id="2"
                       display_name="test_history"/>
                   <metadata
-                      dbkey="hg17"
+                      dbkey="?"
                       data_lines="27"
                       comment_lines="19"
                       columns="9"
@@ -113,11 +113,11 @@
                       />
                   <tool
                       tool_id="upload1"
-                      tool_version="1.1.4"
+                      tool_version="1.1.6"
                       />
                 </metadata>
               </trackFile>
-              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_9.dat" ext="gff3" label="D.gff">
+              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_9.dat" ext="gff3" label="D.gff">
                 <metadata>
                   <dataset id="b842d972534ccb3e" hid="5"
                       size="2.3 KB"
@@ -128,7 +128,7 @@
                       user_id="2"
                       display_name="test_history"/>
                   <metadata
-                      dbkey="hg17"
+                      dbkey="?"
                       data_lines="27"
                       comment_lines="19"
                       columns="9"
@@ -138,7 +138,7 @@
                       />
                   <tool
                       tool_id="upload1"
-                      tool_version="1.1.4"
+                      tool_version="1.1.6"
                       />
                 </metadata>
               </trackFile>
@@ -171,7 +171,7 @@
         </track>
         <track cat="Ignore Scale" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff">
                 <metadata>
                   <dataset id="5449172d6ff5669b" hid="6"
                       size="2.3 KB"
@@ -182,7 +182,7 @@
                       user_id="2"
                       display_name="test_history"/>
                   <metadata
-                      dbkey="hg17"
+                      dbkey="?"
                       data_lines="27"
                       comment_lines="19"
                       columns="9"
@@ -192,7 +192,7 @@
                       />
                   <tool
                       tool_id="upload1"
-                      tool_version="1.1.4"
+                      tool_version="1.1.6"
                       />
                 </metadata>
               </trackFile>
@@ -225,7 +225,7 @@
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff">
                 <metadata>
                   <dataset id="5449172d6ff5669b" hid="6"
                       size="2.3 KB"
@@ -236,7 +236,7 @@
                       user_id="2"
                       display_name="test_history"/>
                   <metadata
-                      dbkey="hg17"
+                      dbkey="?"
                       data_lines="27"
                       comment_lines="19"
                       columns="9"
@@ -246,7 +246,7 @@
                       />
                   <tool
                       tool_id="upload1"
-                      tool_version="1.1.4"
+                      tool_version="1.1.6"
                       />
                 </metadata>
               </trackFile>
@@ -285,7 +285,7 @@
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff">
                 <metadata>
                   <dataset id="5449172d6ff5669b" hid="6"
                       size="2.3 KB"
@@ -296,7 +296,7 @@
                       user_id="2"
                       display_name="test_history"/>
                   <metadata
-                      dbkey="hg17"
+                      dbkey="?"
                       data_lines="27"
                       comment_lines="19"
                       columns="9"
@@ -306,7 +306,7 @@
                       />
                   <tool
                       tool_id="upload1"
-                      tool_version="1.1.4"
+                      tool_version="1.1.6"
                       />
                 </metadata>
               </trackFile>
@@ -345,7 +345,7 @@
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff">
                 <metadata>
                   <dataset id="5449172d6ff5669b" hid="6"
                       size="2.3 KB"
@@ -356,7 +356,7 @@
                       user_id="2"
                       display_name="test_history"/>
                   <metadata
-                      dbkey="hg17"
+                      dbkey="?"
                       data_lines="27"
                       comment_lines="19"
                       columns="9"
@@ -366,7 +366,7 @@
                       />
                   <tool
                       tool_id="upload1"
-                      tool_version="1.1.4"
+                      tool_version="1.1.6"
                       />
                 </metadata>
               </trackFile>
@@ -407,7 +407,7 @@
         </track>
         <track cat="Scaled Colour" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_10.dat" ext="gff3" label="1.gff">
+              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_10.dat" ext="gff3" label="1.gff">
                 <metadata>
                   <dataset id="5449172d6ff5669b" hid="6"
                       size="2.3 KB"
@@ -418,7 +418,7 @@
                       user_id="2"
                       display_name="test_history"/>
                   <metadata
-                      dbkey="hg17"
+                      dbkey="?"
                       data_lines="27"
                       comment_lines="19"
                       columns="9"
@@ -428,7 +428,7 @@
                       />
                   <tool
                       tool_id="upload1"
-                      tool_version="1.1.4"
+                      tool_version="1.1.6"
                       />
                 </metadata>
               </trackFile>
@@ -469,7 +469,7 @@
         </track>
         <track cat="Realistic" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_11.dat" ext="gff3" label="interpro.gff">
+              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_11.dat" ext="gff3" label="interpro.gff">
                 <metadata>
                   <dataset id="9ce08b2254e4d5ed" hid="7"
                       size="103.3 KB"
@@ -480,7 +480,7 @@
                       user_id="2"
                       display_name="test_history"/>
                   <metadata
-                      dbkey="hg17"
+                      dbkey="?"
                       data_lines="556"
                       comment_lines="2"
                       columns="9"
@@ -490,7 +490,7 @@
                       />
                   <tool
                       tool_id="upload1"
-                      tool_version="1.1.4"
+                      tool_version="1.1.6"
                       />
                 </metadata>
               </trackFile>
@@ -523,7 +523,7 @@
         </track>
         <track cat="Realistic" format="gene_calls" visibility="default_off">
             <files>
-              <trackFile path="/tmp/tmpnh6QWY/files/000/dataset_12.dat" ext="gff3" label="2.gff">
+              <trackFile path="/tmp/tmpWtvfKr/files/000/dataset_12.dat" ext="gff3" label="2.gff">
                 <metadata>
                   <dataset id="80b8022ff3f677b7" hid="8"
                       size="326 bytes"
@@ -534,7 +534,7 @@
                       user_id="2"
                       display_name="test_history"/>
                   <metadata
-                      dbkey="hg17"
+                      dbkey="?"
                       data_lines="3"
                       comment_lines="3"
                       columns="9"
@@ -544,7 +544,7 @@
                       />
                   <tool
                       tool_id="upload1"
-                      tool_version="1.1.4"
+                      tool_version="1.1.6"
                       />
                 </metadata>
               </trackFile>
@@ -581,6 +581,7 @@
         ComboTrackSelector=""
         Bookmarks=""
         GCContent=""
+        BlastView="True"
         theme=""
         />
 </root>