Mutable configs on test

files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml

@@ -44,6 +44,7 @@
 
 
 
+
 
 
 <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">
@@ -86,6 +87,7 @@
 
 
 
+
 
 
 <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">
@@ -117,6 +119,7 @@
 
 
 
+
 <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>
@@ -147,6 +150,7 @@
 
 
 
+
 <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>
@@ -176,6 +180,7 @@
 
 
 
+
 <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>
@@ -202,6 +207,7 @@
 
 
 
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/data_manager/twobit_builder/0.0.1" id="twobit_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_twobit_builder/74b09c8e5f6e/data_manager_twobit_builder/data_manager/twobit_builder.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/twobit_builder_data_manager/0.0.1"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_twobit_builder</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>74b09c8e5f6e</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/devteam/data_manager_twobit_builder/twobit_builder_data_manager/0.0.1</id><version>0.0.1</version></tool><data_table name="lastz_seqs">
             <output>
@@ -248,6 +254,7 @@
 
 
 
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/fetch_genome_all_fasta_dbkeys/0.0.1" id="fetch_genome_all_fasta_dbkeys" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml">
         <tool file="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/776bb1b478a0/data_manager_fetch_genome_dbkeys_all_fasta/data_manager/data_manager_fetch_genome_all_fasta_dbkeys.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.1"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_fetch_genome_dbkeys_all_fasta</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>776bb1b478a0</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.1</id><version>0.0.1</version></tool><data_table name="all_fasta">
             <output>
@@ -289,6 +296,7 @@
 
 
 
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/data_manager/bwa_mem_index_builder/0.0.1" id="bwa_mem_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_bwa_mem_index_builder/cb0147ade868/data_manager_bwa_mem_index_builder/data_manager/bwa_mem_index_builder.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager/0.0.1"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_bwa_mem_index_builder</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>cb0147ade868</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bwa_mem_index_builder/bwa_mem_index_builder_data_manager/0.0.1</id><version>0.0.1</version></tool><data_table name="bwa_mem_indexes">
             <output>
@@ -315,6 +323,7 @@
 
 
 
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_picard_index_builder/data_manager/picard_index_builder/0.0.1" id="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_picard_index_builder/00491eabe22b/data_manager_picard_index_builder/data_manager/picard_index_builder.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_picard_index_builder/picard_index_builder_data_manager/0.0.1"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_picard_index_builder</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>00491eabe22b</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/devteam/data_manager_picard_index_builder/picard_index_builder_data_manager/0.0.1</id><version>0.0.1</version></tool><data_table name="picard_indexes">
             <output>
@@ -340,6 +349,7 @@
 
 
 
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/bgruening/data_manager_diamond_database_builder/data_manager/diamond_database_builder/0.0.1" id="diamond_database_builder" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml" version="0.0.1">
         <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/data_manager_diamond_database_builder/ce62d0912b10/data_manager_diamond_database_builder/data_manager/data_manager_diamond_database_builder.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/data_manager_diamond_database_builder/diamond_database_builder/0.0.1"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_diamond_database_builder</repository_name><repository_owner>bgruening</repository_owner><installed_changeset_revision>ce62d0912b10</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/bgruening/data_manager_diamond_database_builder/diamond_database_builder/0.0.1</id><version>0.0.1</version></tool><data_table name="diamond_database">
             <output>
@@ -362,6 +372,7 @@
 
 
 
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder/0.0.1" id="hisat2_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/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/hisat2_index_builder_data_manager/1.0.0"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_hisat2_index_builder</repository_name><repository_owner>iuc</repository_owner><installed_changeset_revision>98a60a4cfb9a</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/hisat2_index_builder_data_manager/1.0.0</id><version>1.0.0</version></tool><data_table name="hisat2_indexes">
             <output>
@@ -384,6 +395,7 @@
 
 
 
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/data_manager/bowtie2_index_builder/2.2.6" id="bowtie2_index_builder" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml" version="2.2.6">
         <tool file="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/e87aeff2cf88/data_manager_bowtie2_index_builder/data_manager/bowtie2_index_builder.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/bowtie2_index_builder_data_manager/2.2.6"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_bowtie2_index_builder</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>e87aeff2cf88</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/devteam/data_manager_bowtie2_index_builder/bowtie2_index_builder_data_manager/2.2.6</id><version>2.2.6</version></tool><data_table name="bowtie2_indexes">
             <output>
@@ -419,6 +431,7 @@
 
 
 
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_bowtie_index_builder/data_manager/bowtie_index_builder/0.0.1" id="bowtie_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/iuc/data_manager_bowtie_index_builder/0a0c648498e2/data_manager_bowtie_index_builder/data_manager/bowtie_index_builder.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_bowtie_index_builder/bowtie_index_builder_data_manager/0.0.2"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_bowtie_index_builder</repository_name><repository_owner>iuc</repository_owner><installed_changeset_revision>0a0c648498e2</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/iuc/data_manager_bowtie_index_builder/bowtie_index_builder_data_manager/0.0.2</id><version>0.0.2</version></tool><data_table name="bowtie_indexes">
             <output>
@@ -439,6 +452,7 @@
 
 
 
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_bowtie_index_builder/data_manager/bowtie_color_space_index_builder/0.0.1" id="bowtie_color_space_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/iuc/data_manager_bowtie_index_builder/0a0c648498e2/data_manager_bowtie_index_builder/data_manager/bowtie_color_space_index_builder.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_bowtie_index_builder/bowtie_color_space_index_builder_data_manager/0.0.2"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_bowtie_index_builder</repository_name><repository_owner>iuc</repository_owner><installed_changeset_revision>0a0c648498e2</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/iuc/data_manager_bowtie_index_builder/bowtie_color_space_index_builder_data_manager/0.0.2</id><version>0.0.2</version></tool><data_table name="bowtie_indexes_color">
             <output>
@@ -459,6 +473,7 @@
 
 
 
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/data_manager/fetch_genome_all_fasta/0.0.1" id="fetch_genome_all_fasta" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml">
         <tool file="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/2ebc856bce29/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/data_manager_fetch_genome_all_fasta/0.0.1"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_fetch_genome_all_fasta</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>2ebc856bce29</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/data_manager_fetch_genome_all_fasta/0.0.1</id><version>0.0.1</version></tool><data_table name="all_fasta">
             <output>
@@ -478,4 +493,52 @@
     </data_manager>
 
 
+
+<data_manager guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/data_manager/data_manager_snpeff_databases/0.0.1" id="data_manager_snpeff_databases" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml">
+    <tool file="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/9ac823a8b328/data_manager_snpeff/data_manager/data_manager_snpEff_databases.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/data_manager_snpeff_databases/4.0.0"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_snpeff</repository_name><repository_owner>iuc</repository_owner><installed_changeset_revision>9ac823a8b328</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/data_manager_snpeff_databases/4.0.0</id><version>4.0.0</version></tool><data_table name="snpeffv_databases">  <!-- Defines a Data Table to be modified. -->
+      <output> <!-- Handle the output of the Data Manager Tool -->
+        <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="version" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="name" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+      </output>
+    </data_table>
+  </data_manager>
+
+<data_manager guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/data_manager/data_manager_snpeff_download/0.0.1" id="data_manager_snpeff_download" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml">
+    <tool file="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/9ac823a8b328/data_manager_snpeff/data_manager/data_manager_snpEff_download.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/data_manager_snpeff_download/4.0.0"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_snpeff</repository_name><repository_owner>iuc</repository_owner><installed_changeset_revision>9ac823a8b328</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/iuc/data_manager_snpeff/data_manager_snpeff_download/4.0.0</id><version>4.0.0</version></tool><data_table name="snpeffv_genomedb">  <!-- Defines a Data Table to be modified. -->
+      <output> <!-- Handle the output of the Data Manager Tool -->
+        <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="version" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="path" output_ref="out_file">
+          <move relativize_symlinks="True" type="directory">
+            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">snpEff/v4_0/data</target>
+          </move>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/snpEff/v4_0/data</value_translation>
+          <value_translation type="function">abspath</value_translation>
+        </column>
+      </output>
+    </data_table>
+    <data_table name="snpeffv_regulationdb">  <!-- Defines a Data Table to be modified. -->
+      <output> <!-- Handle the output of the Data Manager Tool -->
+        <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="version" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="genome" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
+      </output>
+    </data_table>
+    <data_table name="snpeffv_annotations">  <!-- Defines a Data Table to be modified. -->
+      <output> <!-- Handle the output of the Data Manager Tool -->
+        <column name="key" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="version" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="genome" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="value" /> <!-- columns that are going to be specified by the Data Manager Tool -->
+        <column name="name" />  <!-- columns that are going to be specified by the Data Manager Tool -->
+      </output>
+    </data_table>
+  </data_manager>
+
 </data_managers>