Mutable configs from Main

galaxyproject · May 12, 2016 · 2ba1cc6 · 2ba1cc6
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diff --git a/files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml b/files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml
@@ -175,6 +175,21 @@
         <label id="solid" text="AB-SOLiD data" version="" />
     </section>
     <section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.2.3.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.2.3.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.2.3.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.2.3.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.2.3.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.2.3.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.2.3.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.2.3.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.2.3.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.2.3.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.2.3.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.2.3.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.2.3.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.2.3.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.2.3.0" />
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.2.2.0" />
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.2.2.0" />
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.2.2.0" />

diff --git a/files/galaxy/usegalaxy.org/var/shed_tool_conf.xml b/files/galaxy/usegalaxy.org/var/shed_tool_conf.xml
@@ -7056,4 +7056,169 @@
     </tool>
 </section>
 
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/ef5c39e31bb7/deeptools_compute_gc_bias/computeGCBias.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_compute_gc_bias</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>ef5c39e31bb7</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_gc_bias/deeptools_compute_gc_bias/2.2.3.0</id>
+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/6a077ef72dd4/deeptools_plot_coverage/plotCoverage.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_plot_coverage</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>6a077ef72dd4</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.2.3.0</id>
+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/13e1fcf29377/deeptools_plot_correlation/plotCorrelation.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_plot_correlation</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>13e1fcf29377</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_correlation/deeptools_plot_correlation/2.2.3.0</id>
+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/d7bc0cc0ce4b/deeptools_plot_heatmap/plotHeatmap.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_plot_heatmap</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>d7bc0cc0ce4b</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/2.2.3.0</id>
+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/be924b6a79ea/deeptools_plot_pca/plotPCA.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_plot_pca</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>be924b6a79ea</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_pca/deeptools_plot_pca/2.2.3.0</id>
+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/bd0fa7f8824d/deeptools_bigwig_compare/bigwigCompare.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_bigwig_compare</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>bd0fa7f8824d</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bigwig_compare/deeptools_bigwig_compare/2.2.3.0</id>
+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/115aa2cbf152/deeptools_bam_coverage/bamCoverage.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_bam_coverage</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>115aa2cbf152</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.2.3.0</id>
+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/8e41fe2f3661/deeptools_bam_compare/bamCompare.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_bam_compare</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>8e41fe2f3661</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_compare/deeptools_bam_compare/2.2.3.0</id>
+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/b9660f621e82/deeptools_plot_fingerprint/plotFingerprint.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_plot_fingerprint</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>b9660f621e82</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_fingerprint/deeptools_plot_fingerprint/2.2.3.0</id>
+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/b319edc108a7/deeptools_multi_bam_summary/multiBamSummary.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_multi_bam_summary</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>b319edc108a7</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bam_summary/deeptools_multi_bam_summary/2.2.3.0</id>
+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/8587a5caa8a6/deeptools_correct_gc_bias/correctGCBias.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_correct_gc_bias</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>8587a5caa8a6</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_correct_gc_bias/deeptools_correct_gc_bias/2.2.3.0</id>
+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/c175187691cc/deeptools_compute_matrix/computeMatrix.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_compute_matrix</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>c175187691cc</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix/deeptools_compute_matrix/2.2.3.0</id>
+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/a14f74993305/deeptools_bam_pe_fragmentsize/bamPEFragmentSize.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_bam_pe_fragmentsize</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>a14f74993305</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_pe_fragmentsize/deeptools_bam_pe_fragmentsize/2.2.3.0</id>
+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/7b4732d497a3/deeptools_multi_bigwig_summary/multiBigwigSummary.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_multi_bigwig_summary/deeptools_multi_bigwig_summary/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_multi_bigwig_summary</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>7b4732d497a3</installed_changeset_revision>
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+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
+<section id="ngs:_deeptools" name="NGS: DeepTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/af7e456ef4f9/deeptools_plot_profile/plotProfiler.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.2.3.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>deeptools_plot_profile</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>af7e456ef4f9</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/2.2.3.0</id>
+        <version>2.2.3.0</version>
+    </tool>
+</section>
+
 </toolbox>