# HG changeset patch
# User dereeper
# Date 1534252937 14400
# Node ID bd20187f16c5309295c029b60f76c44620936a7e
# Parent  f81b8b6a97fb26cc3f61e9bc7bc4c0ff15bb0d2b
planemo upload commit 11382afe87364aaafb19973470d5066229a6e34f-dirty

diff -r f81b8b6a97fb -r bd20187f16c5 Galaxy-Workflow-Haplotype_analysis.ga
--- a/Galaxy-Workflow-Haplotype_analysis.ga	Tue Aug 14 08:32:12 2018 -0400
+++ b/Galaxy-Workflow-Haplotype_analysis.ga	Tue Aug 14 09:22:17 2018 -0400
@@ -6,7 +6,7 @@
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             "annotation": "", 
-            "content_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/2.0.0", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/2.0.0", 
             "errors": null, 
             "id": 0, 
             "input_connections": {}, 
@@ -37,12 +37,12 @@
                 "top": 247
             }, 
             "post_job_actions": {}, 
-            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/2.0.0", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/vcftools_filter_stats_diversity/sniplay_vcftoolsfilter/2.0.0", 
             "tool_shed_repository": {
                 "changeset_revision": null, 
                 "name": "vcftools_filter_stats_diversity", 
-                "owner": "vmarcon", 
-                "tool_shed": "testtoolshed.g2.bx.psu.edu"
+                "owner": "dereeper", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
             }, 
             "tool_state": "{\"nb_alleles_min\": \"\\\"2\\\"\", \"chromosomes\": \"\\\"3\\\"\", \"__page__\": null, \"nb_alleles_max\": \"\\\"4\\\"\", \"type_p\": \"\\\"ALL\\\"\", \"allow_missing\": \"\\\"1.0\\\"\", \"fileout_label\": \"\\\"filtered\\\"\", \"frequency\": \"\\\"0.001\\\"\", \"export\": \"\\\"VCF\\\"\", \"samples\": \"\\\"\\\"\", \"bound_end\": \"\\\"100000000\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"max_freq\": \"\\\"0.5\\\"\", \"__rerun_remap_job_id__\": null, \"bound_start\": \"\\\"1\\\"\"}", 
             "tool_version": "2.0.0", 
@@ -52,7 +52,7 @@
         }, 
         "1": {
             "annotation": "", 
-            "content_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/beagle/Beagle/1.0.0", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/beagle/Beagle/1.0.0", 
             "errors": null, 
             "id": 1, 
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@@ -84,12 +84,12 @@
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             "post_job_actions": {}, 
-            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/beagle/Beagle/1.0.0", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/beagle/Beagle/1.0.0", 
             "tool_shed_repository": {
                 "changeset_revision": null, 
                 "name": "beagle", 
-                "owner": "vmarcon", 
-                "tool_shed": "testtoolshed.g2.bx.psu.edu"
+                "owner": "dereeper", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
             }, 
             "tool_state": "{\"phase\": \"\\\"5\\\"\", \"__page__\": null, \"__rerun_remap_job_id__\": null, \"impute\": \"\\\"5\\\"\", \"vcf_input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
             "tool_version": "1.0.0", 
@@ -99,7 +99,7 @@
         }, 
         "2": {
             "annotation": "", 
-            "content_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/sniplay/getHaplotypesFromPhasedVCF/2.0.0", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/getHaplotypesFromPhasedVCF/2.0.0", 
             "errors": null, 
             "id": 2, 
             "input_connections": {
@@ -135,12 +135,12 @@
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             }, 
             "post_job_actions": {}, 
-            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/sniplay/getHaplotypesFromPhasedVCF/2.0.0", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/sniplay/getHaplotypesFromPhasedVCF/2.0.0", 
             "tool_shed_repository": {
                 "changeset_revision": null, 
                 "name": "sniplay", 
-                "owner": "vmarcon", 
-                "tool_shed": "testtoolshed.g2.bx.psu.edu"
+                "owner": "dereeper", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
             }, 
             "tool_state": "{\"output_label\": \"\\\"Haplotypes\\\"\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", 
             "tool_version": "2.0.0", 
@@ -150,7 +150,7 @@
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         "3": {
             "annotation": "", 
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+            "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/haplophyle/haplophyle/1.0.0", 
             "errors": null, 
             "id": 3, 
             "input_connections": {
@@ -186,12 +186,12 @@
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             }, 
             "post_job_actions": {}, 
-            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/haplophyle/haplophyle/1.0.0", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/haplophyle/haplophyle/1.0.0", 
             "tool_shed_repository": {
                 "changeset_revision": null, 
                 "name": "haplophyle", 
-                "owner": "vmarcon", 
-                "tool_shed": "testtoolshed.g2.bx.psu.edu"
+                "owner": "dereeper", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
             }, 
             "tool_state": "{\"color\": \"{\\\"__current_case__\\\": 0, \\\"choice\\\": \\\"false\\\"}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", 
             "tool_version": "1.0.0", 
@@ -201,7 +201,7 @@
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         "4": {
             "annotation": "", 
-            "content_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/cytoscape/Cytoscape/1.0.0", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/dereeper/cytoscape/Cytoscape/1.0.0", 
             "errors": null, 
             "id": 4, 
             "input_connections": {
@@ -233,12 +233,12 @@
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             "post_job_actions": {}, 
-            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/vmarcon/cytoscape/Cytoscape/1.0.0", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/dereeper/cytoscape/Cytoscape/1.0.0", 
             "tool_shed_repository": {
                 "changeset_revision": null, 
                 "name": "cytoscape", 
-                "owner": "vmarcon", 
-                "tool_shed": "testtoolshed.g2.bx.psu.edu"
+                "owner": "dereeper", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
             }, 
             "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": null}", 
             "tool_version": "1.0.0",