Pull mutable configs after upgrading sequence tools

galaxyproject · Oct 2, 2017 · b64ae9b · b64ae9b
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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
@@ -104,6 +104,17 @@
         <tool id="gtf_filter_by_attribute_values_list" />
     </section>
     <section id="NGS_QC" name="NGS: QC and manipulation" version="">
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.1.1" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_splitter/fastq_paired_end_splitter/1.1.1" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.1.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.1" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_masker_by_quality/fastq_masker_by_quality/1.1.1" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.1" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.1" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.1" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_combiner/fastq_combiner/1.1.1" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11" />
         <tool id="toolshed.g2.bx.psu.edu/repos/engineson/multiqc/multiqc/1.0.0.0" />
         <tool id="toolshed.g2.bx.psu.edu/repos/lparsons/fastq_join/fastq_join/1.1.2-806.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.1" />
@@ -512,6 +523,9 @@
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_clusterbed/2.22.0" />
     </section>
     <section id="convert" name="Convert Formats" version="">
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.1.1" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.1" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.0.0" />
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.0" />
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.0.0" />
@@ -920,6 +934,7 @@
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_segmasker_wrapper/0.1.08" />
     </section>
     <section id="ngs:_assembly" name="NGS: Assembly" version="">
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0" />
         <tool id="testtoolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.2.0" />
         <tool id="toolshed.g2.bx.psu.edu/repos/peterjc/mummer/mummerplot_wrapper/0.0.5" />

diff --git a/env/test/files/galaxy/var/shed_tool_conf.xml b/env/test/files/galaxy/var/shed_tool_conf.xml
@@ -8968,4 +8968,169 @@
     </tool>
 </section>
 
+<section id="NGS_QC" name="NGS: QC and manipulation" version="">
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+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>flash</repository_name>
+        <repository_owner>iuc</repository_owner>
+        <installed_changeset_revision>13e98e2709b8</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11</id>
+        <version>1.2.11</version>
+    </tool>
+</section>
+
+<section id="ngs:_assembly" name="NGS: Assembly" version="">
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+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>unicycler</repository_name>
+        <repository_owner>iuc</repository_owner>
+        <installed_changeset_revision>f13d0498a199</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.1</id>
+        <version>0.4.1</version>
+    </tool>
+</section>
+
+<section id="NGS_QC" name="NGS: QC and manipulation" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/fastq_combiner/56389130cb63/fastq_combiner/fastq_combiner.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/fastq_combiner/fastq_combiner/1.1.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>fastq_combiner</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>56389130cb63</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/fastq_combiner/fastq_combiner/1.1.1</id>
+        <version>1.1.1</version>
+    </tool>
+</section>
+
+<section id="NGS_QC" name="NGS: QC and manipulation" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/06934412f56d/fastq_filter/fastq_filter.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>fastq_filter</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>06934412f56d</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/fastq_filter/fastq_filter/1.1.1</id>
+        <version>1.1.1</version>
+    </tool>
+</section>
+
+<section id="NGS_QC" name="NGS: QC and manipulation" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/71e5fa25b8a2/fastq_groomer/fastq_groomer.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>fastq_groomer</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>71e5fa25b8a2</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/fastq_groomer/fastq_groomer/1.1.1</id>
+        <version>1.1.1</version>
+    </tool>
+</section>
+
+<section id="NGS_QC" name="NGS: QC and manipulation" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/4ac14b275aca/fastq_manipulation/fastq_manipulation.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>fastq_manipulation</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>4ac14b275aca</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.1</id>
+        <version>1.1.1</version>
+    </tool>
+</section>
+
+<section id="NGS_QC" name="NGS: QC and manipulation" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/fastq_masker_by_quality/eb592e9ec47a/fastq_masker_by_quality/fastq_masker_by_quality.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/fastq_masker_by_quality/fastq_masker_by_quality/1.1.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>fastq_masker_by_quality</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>eb592e9ec47a</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/fastq_masker_by_quality/fastq_masker_by_quality/1.1.1</id>
+        <version>1.1.1</version>
+    </tool>
+</section>
+
+<section id="NGS_QC" name="NGS: QC and manipulation" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/462abc5618ba/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>fastq_paired_end_deinterlacer</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>462abc5618ba</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_deinterlacer/fastq_paired_end_deinterlacer/1.1.1</id>
+        <version>1.1.1</version>
+    </tool>
+</section>
+
+<section id="NGS_QC" name="NGS: QC and manipulation" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/effda79f510c/fastq_paired_end_interlacer/fastq_paired_end_interlacer.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>fastq_paired_end_interlacer</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>effda79f510c</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_interlacer/fastq_paired_end_interlacer/1.2.0</id>
+        <version>1.2.0</version>
+    </tool>
+</section>
+
+<section id="NGS_QC" name="NGS: QC and manipulation" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/080a058abf1e/fastq_paired_end_joiner/fastq_paired_end_joiner.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.1.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>fastq_paired_end_joiner</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>080a058abf1e</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_joiner/fastq_paired_end_joiner/2.0.1.0</id>
+        <version>2.0.1.0</version>
+    </tool>
+</section>
+
+<section id="NGS_QC" name="NGS: QC and manipulation" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_splitter/9bbe5b7ffa12/fastq_paired_end_splitter/fastq_paired_end_splitter.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_splitter/fastq_paired_end_splitter/1.1.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>fastq_paired_end_splitter</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>9bbe5b7ffa12</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/fastq_paired_end_splitter/fastq_paired_end_splitter/1.1.1</id>
+        <version>1.1.1</version>
+    </tool>
+</section>
+
+<section id="NGS_QC" name="NGS: QC and manipulation" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/e2cf940128d5/fastq_stats/fastq_stats.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.1.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>fastq_stats</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>e2cf940128d5</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/fastq_stats/fastq_stats/1.1.1</id>
+        <version>1.1.1</version>
+    </tool>
+</section>
+
+<section id="convert" name="Convert Formats" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/ccf4e1d1fcbe/fastq_to_tabular/fastq_to_tabular.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>fastq_to_tabular</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>ccf4e1d1fcbe</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_tabular/fastq_to_tabular/1.1.1</id>
+        <version>1.1.1</version>
+    </tool>
+</section>
+
+<section id="convert" name="Convert Formats" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/4844c1810c16/fastqtofasta/fastq_to_fasta.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>fastqtofasta</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>4844c1810c16</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/fastqtofasta/fastq_to_fasta_python/1.1.1</id>
+        <version>1.1.1</version>
+    </tool>
+</section>
+
+<section id="convert" name="Convert Formats" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/b8cdc0507586/tabular_to_fastq/tabular_to_fastq.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.1.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>tabular_to_fastq</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>b8cdc0507586</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq/1.1.1</id>
+        <version>1.1.1</version>
+    </tool>
+</section>
+
 </toolbox>