Test mutable configs

galaxyproject · Oct 9, 2015 · a17ff1e · a17ff1e
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diff --git a/files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml b/files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml
@@ -150,6 +150,7 @@
         <tool id="toolshed.g2.bx.psu.edu/repos/nilshomer/tmap_wrapper/tmap_wrapper/0.0.19" />
     </section>
     <section id="ngs-rna-tools" name="NGS: RNA Analysis" version="">
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/cummerbund/cummeRbund/1.0.0" />
         <tool id="toolshed.g2.bx.psu.edu/repos/nate/trinity_psc/trinity_psc/0.0.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/hisat/hisat/1.0.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/cuffdiff/cuffdiff/2.2.1.2" />
@@ -811,6 +812,7 @@
         <tool id="toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/heteroprob/2.0.0" />
     </section>
     <section id="metagenomics" name="Metagenomics" version="">
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/Kraken2Tax/1.1" />
         <tool id="testtoolshed.g2.bx.psu.edu/repos/iuc/vegan_fisher_alpha/vegan_fisher_alpha/0.0.1" />
         <tool id="testtoolshed.g2.bx.psu.edu/repos/iuc/vegan_diversity/vegan_diversity/0.0.1" />
         <tool id="testtoolshed.g2.bx.psu.edu/repos/iuc/vegan_rarefaction/vegan_rarefaction/0.0.1" />

diff --git a/files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml b/files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml
@@ -36,6 +36,7 @@
 
 
 
+
 
 
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/data_manager/data_manager_gemini_download/0.0.1" id="data_manager_gemini_download" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml">
@@ -73,6 +74,7 @@
 
 
 
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/data_manager/sam_fasta_index_builder/0.0.1" id="sam_fasta_index_builder" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml" version="0.0.1">
         <tool file="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/cf875cbe2df4/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/sam_fasta_index_builder/0.0.2"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_sam_fasta_index_builder</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>cf875cbe2df4</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/sam_fasta_index_builder/0.0.2</id><version>0.0.2</version></tool><data_table name="fasta_indexes">
             <output>
@@ -104,6 +106,7 @@
 
 
 
+
 <data_manager guid="testtoolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/data_manager/kraken_database_builder/1.0.0" id="kraken_database_builder" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml" version="1.0.0">
         <tool file="testtoolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/d5d803e654dd/data_manager_build_kraken_database/data_manager/kraken_database_builder.xml" guid="testtoolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/kraken_database_builder/1.0.0"><tool_shed>testtoolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_build_kraken_database</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>d5d803e654dd</installed_changeset_revision><id>testtoolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/kraken_database_builder/1.0.0</id><version>1.0.0</version></tool><data_table name="kraken_databases">
             <output>
@@ -122,6 +125,7 @@
 
 
 
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/data_manager/gatk_picard_index_builder/0.0.1" id="gatk_picard_index_builder" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml" version="0.0.1">
         <tool file="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/700f2df51eb0/data_manager_gatk_picard_index_builder/data_manager/data_manager_gatk_picard_index_builder.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/gatk_picard_index_builder/0.0.1"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_gatk_picard_index_builder</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>700f2df51eb0</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/devteam/data_manager_gatk_picard_index_builder/gatk_picard_index_builder/0.0.1</id><version>0.0.1</version></tool><data_table name="gatk_picard_indexes">
             <output>
@@ -141,6 +145,7 @@
     </data_manager>
 
 
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_hisat_index_builder/data_manager/hisat_index_builder/0.0.1" id="hisat_index_builder" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml" version="0.0.1">
         <tool file="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_hisat_index_builder/ba11fef120cd/data_manager_hisat_index_builder/data_manager/hisat_index_builder.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_hisat_index_builder/hisat_index_builder_data_manager/1.0.0"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_hisat_index_builder</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>ba11fef120cd</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/devteam/data_manager_hisat_index_builder/hisat_index_builder_data_manager/1.0.0</id><version>1.0.0</version></tool><data_table name="hisat_indexes">
             <output>
@@ -159,4 +164,21 @@
         </data_table>
     </data_manager>
 
+
+<data_manager guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_ncbi_taxonomy/data_manager/ncbi_taxonomy_fetcher/1.0.0" id="ncbi_taxonomy_fetcher" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml" version="1.0.0">
+        <tool file="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_ncbi_taxonomy/fafcd2f5db36/data_manager_fetch_ncbi_taxonomy/data_manager/ncbi_taxonomy_fetcher.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_ncbi_taxonomy/ncbi_taxonomy_fetcher/1.0.0"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_fetch_ncbi_taxonomy</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>fafcd2f5db36</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_ncbi_taxonomy/ncbi_taxonomy_fetcher/1.0.0</id><version>1.0.0</version></tool><data_table name="ncbi_taxonomy">
+            <output>
+                <column name="value" />
+                <column name="name" />
+                <column name="path" output_ref="out_file">
+                    <move relativize_symlinks="True" type="directory">
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">ncbi_taxonomy/${value}</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/ncbi_taxonomy/${value}</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
+    </data_manager>
+
 </data_managers>
diff --git a/files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml b/files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml
@@ -6529,4 +6529,15 @@
     </tool>
 </section>
 
+<section id="metagenomics" name="Metagenomics" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/d844fdcce44e/kraken2tax/kraken2tax.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/Kraken2Tax/1.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>kraken2tax</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>d844fdcce44e</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/Kraken2Tax/1.1</id>
+        <version>1.1</version>
+    </tool>
+</section>
+
 </toolbox>
diff --git a/files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml b/files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml
@@ -1190,4 +1190,24 @@
             <installed_changeset_revision>3a3234d7a2e8</installed_changeset_revision>
             </tool_shed_repository>
     </table>
+<table comment_char="#" name="ncbi_taxonomy">
+        <columns>value, name, path</columns>
+        <file path="/galaxy-repl/test/tool_data/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_ncbi_taxonomy/fafcd2f5db36/ncbi_taxonomy.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>data_manager_fetch_ncbi_taxonomy</repository_name>
+            <repository_owner>devteam</repository_owner>
+            <installed_changeset_revision>fafcd2f5db36</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="ncbi_taxonomy">
+        <columns>value, name, path</columns>
+        <file path="/galaxy-repl/test/tool_data/toolshed.g2.bx.psu.edu/repos/devteam/kraken2tax/d844fdcce44e/ncbi_taxonomy.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>kraken2tax</repository_name>
+            <repository_owner>devteam</repository_owner>
+            <installed_changeset_revision>d844fdcce44e</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
 </tables>