Mutable configs for updated sequence utils

galaxyproject · Oct 2, 2017 · c89e745 · c89e745
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diff --git a/env/main/files/galaxy/var/integrated_tool_panel.xml b/env/main/files/galaxy/var/integrated_tool_panel.xml
@@ -92,6 +92,9 @@
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     </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/iuc/bam_to_scidx/bam_to_scidx/1.0.0" />
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@@ -140,6 +143,16 @@
         <tool id="Extract genomic DNA 1" />
     </section>
     <section id="cshl_library_information" 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" />
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diff --git a/env/main/files/galaxy/var/shed_tool_conf.xml b/env/main/files/galaxy/var/shed_tool_conf.xml
@@ -11987,4 +11987,147 @@
     </tool>
 </section>
 
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+        <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>
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+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>fastq_groomer</repository_name>
+        <repository_owner>devteam</repository_owner>
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+      <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>
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+      <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="cshl_library_information" 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">
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+        <repository_name>fastq_paired_end_deinterlacer</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>462abc5618ba</installed_changeset_revision>
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+        <version>1.1.1</version>
+    </tool>
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+<section id="cshl_library_information" 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">
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+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>080a058abf1e</installed_changeset_revision>
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+
+<section id="cshl_library_information" name="NGS: QC and manipulation" version="">
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+        <repository_owner>devteam</repository_owner>
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+</section>
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+  <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>
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+<section id="convert" name="Convert Formats" version="">
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+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
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+        <repository_owner>devteam</repository_owner>
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+</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>
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+        <repository_owner>devteam</repository_owner>
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+        <version>1.1.1</version>
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+<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>
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+        <repository_owner>devteam</repository_owner>
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+    </tool>
+</section>
+
 </toolbox>