Test mutable configs

galaxyproject · Nov 5, 2018 · 00c9258 · 00c9258
1 parent 86c430e
commit 00c9258
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diff --git a/env/test/files/galaxy/var/integrated_tool_panel.xml b/env/test/files/galaxy/var/integrated_tool_panel.xml
@@ -413,6 +413,10 @@
 
     <section id="solexa_tools" name="NGS: Mapping" version="">
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6" />
@@ -2329,4 +2333,14 @@
 
     </section>
 
+    <section id="ncbi_sra" name="NCBI SRA" version="">
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.9.1.3" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.9.1.2" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.9.1.3" />
+
+    </section>
+
 </toolbox>
diff --git a/env/test/files/galaxy/var/shed_tool_conf.xml b/env/test/files/galaxy/var/shed_tool_conf.xml
@@ -8130,4 +8130,48 @@
             <version>0.7.0.3</version>
         </tool>
     </section>
+    <section id="ncbi_sra" name="NCBI SRA" version="">
+        <tool file="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/c38286ea7047/sra_tools/sam_dump.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.9.1.3">
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>sra_tools</repository_name>
+            <repository_owner>iuc</repository_owner>
+            <installed_changeset_revision>c38286ea7047</installed_changeset_revision>
+            <id>toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump/2.9.1.3</id>
+            <version>2.9.1.3</version>
+        </tool>
+        <tool file="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/c38286ea7047/sra_tools/sra_pileup.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.9.1.2">
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>sra_tools</repository_name>
+            <repository_owner>iuc</repository_owner>
+            <installed_changeset_revision>c38286ea7047</installed_changeset_revision>
+            <id>toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup/2.9.1.2</id>
+            <version>2.9.1.2</version>
+        </tool>
+        <tool file="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/c38286ea7047/sra_tools/fastq_dump.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.9.1.3">
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>sra_tools</repository_name>
+            <repository_owner>iuc</repository_owner>
+            <installed_changeset_revision>c38286ea7047</installed_changeset_revision>
+            <id>toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump/2.9.1.3</id>
+            <version>2.9.1.3</version>
+        </tool>
+    </section>
+    <section id="solexa_tools" name="NGS: Mapping" version="">
+        <tool file="toolshed.g2.bx.psu.edu/repos/devteam/bwa/8d2a528a9513/bwa/bwa-mem.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1">
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>bwa</repository_name>
+            <repository_owner>devteam</repository_owner>
+            <installed_changeset_revision>8d2a528a9513</installed_changeset_revision>
+            <id>toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.1</id>
+            <version>0.7.17.1</version>
+        </tool>
+        <tool file="toolshed.g2.bx.psu.edu/repos/devteam/bwa/8d2a528a9513/bwa/bwa.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4">
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>bwa</repository_name>
+            <repository_owner>devteam</repository_owner>
+            <installed_changeset_revision>8d2a528a9513</installed_changeset_revision>
+            <id>toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4</id>
+            <version>0.7.17.4</version>
+        </tool>
+    </section>
 </toolbox>
diff --git a/env/test/files/galaxy/var/shed_tool_data_table_conf.xml b/env/test/files/galaxy/var/shed_tool_data_table_conf.xml
@@ -3170,4 +3170,14 @@
             <installed_changeset_revision>836d1aa3e89a</installed_changeset_revision>
         </tool_shed_repository>
     </table>
+    <table comment_char="#" name="bwa_mem_indexes">
+        <columns>value, dbkey, name, path</columns>
+        <file path="/cvmfs/test.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/devteam/bwa/8d2a528a9513/bwa_mem_index.loc"/>
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>bwa</repository_name>
+            <repository_owner>devteam</repository_owner>
+            <installed_changeset_revision>8d2a528a9513</installed_changeset_revision>
+        </tool_shed_repository>
+    </table>
 </tables>