Mercurial > repos > iuc > jbrowse

changeset 19:8f33c9fbc119 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
author iuc
date Fri, 06 Jul 2018 06:10:18 -0400
parents 836d1aa3e89a
children 558d652cd681
files jbrowse.xml macros.xml test-data/bam/154.bam test-data/bam/154.bam.bai test-data/bam/merlin-sample.bam test-data/bam/merlin-sample.bam.bai test-data/bam/test.xml
diffstat 7 files changed, 91 insertions(+), 26 deletions(-) [+]
line wrap: on
line diff
--- a/jbrowse.xml	Thu Nov 16 09:44:45 2017 -0500
+++ b/jbrowse.xml	Fri Jul 06 06:10:18 2018 -0400
@@ -1,4 +1,4 @@
-<tool id="jbrowse" name="JBrowse" version="@WRAPPER_VERSION@.3">
+<tool id="jbrowse" name="JBrowse" version="@TOOL_VERSION@+@WRAPPER_VERSION@">
   <description>genome browser</description>
   <macros>
     <import>macros.xml</import>
@@ -601,7 +601,7 @@
       <param name="gencode" value="1" />
       <param name="standalone" value="Data Directory" />
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gencode/test-1.xml" lines_diff="4" />
+      <output name="output" file="gencode/test-1.xml" lines_diff="14"/>
     </test>
     <test>
       <param name="reference_genome|genome_type_select" value="history"/>
@@ -805,7 +805,7 @@
       </repeat>
 
       <param name="uglyTestingHack" value="enabled" />
-      <output name="output" file="gff3/test.xml" lines_diff="64" />
+      <output name="output" file="gff3/test.xml" lines_diff="256" />
     </test>
     <test>
         <param name="reference_genome|genome_type_select" value="history"/>
@@ -908,13 +908,33 @@
         <output name="output" file="track_config/test.xml" lines_diff="26"/>
     </test>
     <test>
+        <param name="reference_genome|genome_type_select" value="history"/>
+        <param name="reference_genome|genomes" value="merlin.fa"/>
+        <param name="gencode" value="11" />
+        <param name="standalone" value="Data Directory" />
+
+        <repeat name="track_groups">
+            <param name="category" value="Auto Coloured" />
+            <repeat name="data_tracks">
+                <conditional name="data_format">
+                    <param name="data_format_select" value="pileup"/>
+                    <param name="annotation" value="bam/merlin-sample.bam"/>
+                </conditional>
+            </repeat>
+        </repeat>
+
+        <param name="uglyTestingHack" value="enabled" />
+        <output name="output" file="bam/test.xml" lines_diff="48"/>
+    </test>
+
+    <test>
         <!-- data_table -->
         <param name="reference_genome|genome_type_select" value="indexed"/>
         <param name="reference_genome|genomes" value="merlin"/>
         <param name="gencode" value="1" />
         <param name="standalone" value="Data Directory" />
         <param name="uglyTestingHack" value="enabled" />
-        <output name="output" file="gencode/test-data_table.xml" lines_diff="4" />
+        <output name="output" file="gencode/test-data_table.xml" lines_diff="6" />
     </test>
   </tests>
   <help><![CDATA[
--- a/macros.xml	Thu Nov 16 09:44:45 2017 -0500
+++ b/macros.xml	Fri Jul 06 06:10:18 2018 -0400
@@ -1,8 +1,9 @@
 <?xml version="1.0"?>
 <macros>
+  <token name="@TOOL_VERSION@">1.12.5</token>
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="1.12.3">jbrowse</requirement>
+      <requirement type="package" version="@TOOL_VERSION@">jbrowse</requirement>
       <requirement type="package" version="2.7">python</requirement>
       <requirement type="package" version="1.66">biopython</requirement>
       <requirement type="package" version="0.6.2">bcbiogff</requirement>
@@ -12,7 +13,7 @@
     </requirements>
   </xml>
   <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token>
-  <token name="@WRAPPER_VERSION@">0.7.0</token>
+  <token name="@WRAPPER_VERSION@">galaxy0</token>
   <xml name="stdio">
     <stdio>
       <exit_code range="1:"/>
Binary file test-data/bam/154.bam has changed
Binary file test-data/bam/154.bam.bai has changed
Binary file test-data/bam/merlin-sample.bam has changed
Binary file test-data/bam/merlin-sample.bam.bai has changed
--- a/test-data/bam/test.xml	Thu Nov 16 09:44:45 2017 -0500
+++ b/test-data/bam/test.xml	Fri Jul 06 06:10:18 2018 -0400
@@ -3,46 +3,90 @@
     <metadata>
         <gencode>11</gencode>
         <genomes>
-            <genome>test-data/merlin.fa</genome>
+                  <genome path="/tmp/tmpfqQZDj/files/000/dataset_2.dat">
+                    <metadata>
+                      <dataset id="9a22496ee796fbfc" hid="1"
+                          size="171.6 KB"
+                          edam_format="format_1929"
+                          file_ext="fasta" />
+                      <history id="fa6d20d0fb68383f"
+                          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>
-            <trackPadding>40</trackPadding>
+            <trackPadding>20</trackPadding>
+
             <shareLink>true</shareLink>
             <aboutDescription></aboutDescription>
             <show_tracklist>true</show_tracklist>
             <show_nav>true</show_nav>
-            <show_overview>false</show_overview>
+            <show_overview>true</show_overview>
             <show_menu>true</show_menu>
             <hideGenomeOptions>false</hideGenomeOptions>
         </general>
+        <galaxyUrl>http://localhost</galaxyUrl>
     </metadata>
     <tracks>
-        <track cat="Default" format="pileup">
+        <track cat="Aligned reads" format="pileup" visibility="default_off">
             <files>
-                <trackFile path="test-data/bam/154.bam" ext="bam" label="Basic"/>
+              <trackFile path="/tmp/tmpfqQZDj/files/000/dataset_1.dat" ext="bam" label="merlin-sample.bam">
+                <metadata>
+                  <dataset id="2891970512fa2d5a" hid="1"
+                      size="12.9 KB"
+                      edam_format="format_2572"
+                      file_ext="bam" />
+                  <history id="2891970512fa2d5a"
+                      user_email="planemo@galaxyproject.org"
+                      user_id="1"
+                      display_name="Unnamed history"/>
+                  <metadata
+                      dbkey="hg17"
+                      bam_index="__lt__galaxy.model.MetadataFile object at 0x7fc42c1d18d0__gt__"
+                      bam_version="1.3"
+                      sort_order="coordinate"
+                      read_groups=""
+                      reference_names="[SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7fc4484b3170 on: u__sq__Merlin__sq__]"
+                      reference_lengths="[172788]"
+                      bam_header="{SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7fc44857fb90 on: u__sq__SQ__sq__: [{SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7fc44857fe90 on: u__sq__LN__sq__: 172788, 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object at 7fc44857f230 on: u__sq__HD__sq__: {SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7fc44857f110 on: u__sq__SO__sq__: SafeStringWrapper(unicode:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7fc44857f410 on: u__sq__coordinate__sq__, 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+                      columns="12"
+                      column_names="[SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7fc448337b50 on: __sq__QNAME__sq__, SafeStringWrapper(str:__lt__class __sq__galaxy.tools.wrappers.ToolParameterValueWrapper__sq____gt__,__lt__class __sq__galaxy.util.object_wrapper.SafeStringWrapper__sq____gt__,__lt__class __sq__numbers.Number__sq____gt__,__lt__type __sq__NoneType__sq____gt__,__lt__type __sq__NotImplementedType__sq____gt__,__lt__type __sq__bool__sq____gt__,__lt__type __sq__bytearray__sq____gt__,__lt__type __sq__ellipsis__sq____gt__) object at 7fc448337838 on: __sq__FLAG__sq__, SafeStringWrapper(str:__lt__class 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+                      />
+                  <tool
+                      tool_id="upload1"
+                      tool_version="1.1.4"
+                      />
+                </metadata>
+              </trackFile>
             </files>
+
             <options>
+
                 <pileup>
                     <auto_snp>false</auto_snp>
                     <bam_indices>
-                        <bam_index>test-data/bam/154.bam.bai</bam_index>
-                    </bam_indices>
-                </pileup>
-            </options>
-        </track>
-        <track cat="Default" format="pileup">
-            <files>
-                <trackFile path="test-data/bam/154.bam" ext="bam" label="Auto-SNP"/>
-            </files>
-            <options>
-                <pileup>
-                    <auto_snp>true</auto_snp>
-                    <bam_indices>
-                        <bam_index>test-data/bam/154.bam.bai</bam_index>
+                        <bam_index>/tmp/tmpfqQZDj/files/_metadata_files/000/metadata_1.dat</bam_index>
                     </bam_indices>
                 </pileup>
             </options>
         </track>
     </tracks>
-</root>
+    <plugins
+        ComboTrackSelector=""
+        Bookmarks=""
+        GCContent=""
+        theme=""
+        />
+</root>
\ No newline at end of file