changeset 3:f8221945b946 draft default tip

Uploaded
author urgi-team
date Thu, 26 May 2016 09:27:07 -0400
parents bfd4dc7f50c5
children
files TEiso/Galaxy-Workflow-TEiso_workflow.ga TEiso/repository_dependencies.xml Teiso-workflow-final/Galaxy-Workflow-TEiso_workflow.ga Teiso-workflow-final/repository_dependencies.xml
diffstat 4 files changed, 446 insertions(+), 446 deletions(-) [+]
line wrap: on
line diff
--- a/TEiso/Galaxy-Workflow-TEiso_workflow.ga	Wed May 25 10:28:25 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,439 +0,0 @@
-{
-    "a_galaxy_workflow": "true", 
-    "annotation": "", 
-    "format-version": "0.1", 
-    "name": "TEiso_workflow", 
-    "steps": {
-        "0": {
-            "annotation": "", 
-            "id": 0, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Input Dataset"
-                }
-            ], 
-            "label": null, 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 200, 
-                "top": 200
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Input Dataset\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": [], 
-            "uuid": "a910dd6c-d6e5-4d3a-b3cd-3624c8c509b6"
-        }, 
-        "1": {
-            "annotation": "", 
-            "id": 1, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Input Dataset"
-                }
-            ], 
-            "label": null, 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 200, 
-                "top": 285
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Input Dataset\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": [], 
-            "uuid": "98cee5d8-d791-4f91-8f29-ccc98003e392"
-        }, 
-        "2": {
-            "annotation": "", 
-            "id": 2, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Input Dataset"
-                }
-            ], 
-            "label": null, 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 200, 
-                "top": 370
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Input Dataset\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": [], 
-            "uuid": "1fc62c7e-fbb8-48b4-89da-18c629838b7c"
-        }, 
-        "3": {
-            "annotation": "", 
-            "id": 3, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Input Dataset"
-                }
-            ], 
-            "label": null, 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 200, 
-                "top": 455
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Input Dataset\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": [], 
-            "uuid": "49264998-41ff-4776-81f2-06e3fbaac133"
-        }, 
-        "4": {
-            "annotation": "", 
-            "id": 4, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "", 
-                    "name": "Input Dataset"
-                }
-            ], 
-            "label": null, 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 200, 
-                "top": 540
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Input Dataset\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": [], 
-            "uuid": "869588d6-af39-40d2-afaa-86a3c9935aa9"
-        }, 
-        "5": {
-            "annotation": "", 
-            "id": 5, 
-            "input_connections": {
-                "refGenomeSource|ownFile": {
-                    "id": 3, 
-                    "output_name": "output"
-                }, 
-                "singlePaired|input1": {
-                    "id": 0, 
-                    "output_name": "output"
-                }, 
-                "singlePaired|input2": {
-                    "id": 1, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
-            "label": null, 
-            "name": "TopHat", 
-            "outputs": [
-                {
-                    "name": "align_summary", 
-                    "type": "txt"
-                }, 
-                {
-                    "name": "fusions", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "insertions", 
-                    "type": "bed"
-                }, 
-                {
-                    "name": "deletions", 
-                    "type": "bed"
-                }, 
-                {
-                    "name": "junctions", 
-                    "type": "bed"
-                }, 
-                {
-                    "name": "accepted_hits", 
-                    "type": "bam"
-                }, 
-                {
-                    "name": "unmapped", 
-                    "type": "bam"
-                }
-            ], 
-            "position": {
-                "left": 428, 
-                "top": 200
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9", 
-            "tool_state": "{\"__page__\": 0, \"singlePaired\": \"{\\\"input2\\\": null, \\\"input1\\\": null, \\\"report_discordant_pairs\\\": \\\"Yes\\\", \\\"sPaired\\\": \\\"paired\\\", \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": \\\"300\\\", \\\"mate_std_dev\\\": \\\"20\\\"}\", \"chromInfo\": \"\\\"/home/repet_cloud/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"readGroup\": \"{\\\"__current_case__\\\": 1, \\\"specReadGroup\\\": \\\"no\\\"}\", \"params\": \"{\\\"settingsType\\\": \\\"preSet\\\", \\\"__current_case__\\\": 0}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\"}", 
-            "tool_version": "0.9", 
-            "type": "tool", 
-            "user_outputs": [], 
-            "uuid": "3b5324aa-7209-4de0-9135-a267ae3d6266"
-        }, 
-        "6": {
-            "annotation": "", 
-            "id": 6, 
-            "input_connections": {
-                "inputFile": {
-                    "id": 4, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
-            "label": null, 
-            "name": "GFFToBed", 
-            "outputs": [
-                {
-                    "name": "outputFile", 
-                    "type": "bed"
-                }
-            ], 
-            "position": {
-                "left": 1071, 
-                "top": 535
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/teiso/GFFToBed/1.0", 
-            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/repet_cloud/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", 
-            "tool_version": "1.0", 
-            "type": "tool", 
-            "user_outputs": [], 
-            "uuid": "ac60365f-0928-44d8-9829-5a616ab7ab23"
-        }, 
-        "7": {
-            "annotation": "", 
-            "id": 7, 
-            "input_connections": {
-                "input": {
-                    "id": 5, 
-                    "output_name": "accepted_hits"
-                }
-            }, 
-            "inputs": [], 
-            "label": null, 
-            "name": "Cufflinks", 
-            "outputs": [
-                {
-                    "name": "genes_expression", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "transcripts_expression", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "assembled_isoforms", 
-                    "type": "gtf"
-                }, 
-                {
-                    "name": "total_map_mass", 
-                    "type": "txt"
-                }, 
-                {
-                    "name": "skipped", 
-                    "type": "gtf"
-                }
-            ], 
-            "position": {
-                "left": 740, 
-                "top": 200
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.0", 
-            "tool_state": "{\"reference_annotation\": \"{\\\"use_ref\\\": \\\"No\\\", \\\"__current_case__\\\": 0}\", \"min_isoform_fraction\": \"\\\"0.1\\\"\", \"multiread_correct\": \"\\\"No\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"pre_mrna_fraction\": \"\\\"0.15\\\"\", \"bias_correction\": \"{\\\"do_bias_correction\\\": \\\"No\\\", \\\"__current_case__\\\": 1}\", \"max_intron_len\": \"\\\"300000\\\"\", \"input\": \"null\", \"global_model\": \"null\", \"chromInfo\": \"\\\"/home/repet_cloud/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"length_correction\": \"\\\"\\\"\", \"advanced_settings\": \"{\\\"__current_case__\\\": 0, \\\"use_advanced_settings\\\": \\\"No\\\"}\"}", 
-            "tool_version": "2.2.1.0", 
-            "type": "tool", 
-            "user_outputs": [], 
-            "uuid": "3a0017dc-8664-49a9-8963-5323cf575ef3"
-        }, 
-        "8": {
-            "annotation": "", 
-            "id": 8, 
-            "input_connections": {
-                "inputFile": {
-                    "id": 7, 
-                    "output_name": "assembled_isoforms"
-                }
-            }, 
-            "inputs": [], 
-            "label": null, 
-            "name": "CufflinksGTFToBed", 
-            "outputs": [
-                {
-                    "name": "outputFile", 
-                    "type": "bed"
-                }
-            ], 
-            "position": {
-                "left": 1068, 
-                "top": 200
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/teiso/CufflinksGTFToBed/1.0", 
-            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/repet_cloud/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"inputFile\": \"null\"}", 
-            "tool_version": "1.0", 
-            "type": "tool", 
-            "user_outputs": [], 
-            "uuid": "97f9cf7e-4f21-4827-81d2-03bd7b66010a"
-        }, 
-        "9": {
-            "annotation": "", 
-            "id": 9, 
-            "input_connections": {
-                "annotation|reference_annotation": {
-                    "id": 2, 
-                    "output_name": "output"
-                }, 
-                "inputs": {
-                    "id": 7, 
-                    "output_name": "skipped"
-                }, 
-                "seq_data|seq_source|ref_file": {
-                    "id": 3, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
-            "label": null, 
-            "name": "Cuffcompare", 
-            "outputs": [
-                {
-                    "name": "transcripts_accuracy", 
-                    "type": "txt"
-                }, 
-                {
-                    "name": "input1_tmap", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "input1_refmap", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "input2_tmap", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "input2_refmap", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "transcripts_tracking", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "transcripts_combined", 
-                    "type": "gtf"
-                }
-            ], 
-            "position": {
-                "left": 1076, 
-                "top": 716
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/cuffcompare/cuffcompare/2.2.1.0", 
-            "tool_state": "{\"seq_data\": \"{\\\"use_seq_data\\\": \\\"Yes\\\", \\\"seq_source\\\": {\\\"index_source\\\": \\\"history\\\", \\\"ref_file\\\": null, \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1}\", \"inputs\": \"null\", \"max_dist_group\": \"\\\"100\\\"\", \"__page__\": 0, \"discard_intron_redundant_transfrags\": \"\\\"False\\\"\", \"max_dist_exon\": \"\\\"100\\\"\", \"__rerun_remap_job_id__\": null, \"additional_inputs\": \"[]\", \"discard_single_exon\": \"\\\"\\\"\", \"chromInfo\": \"\\\"/home/repet_cloud/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"annotation\": \"{\\\"reference_annotation\\\": null, \\\"use_ref_annotation\\\": \\\"Yes\\\", \\\"ignore_nonoverlapping_reference\\\": \\\"False\\\", \\\"__current_case__\\\": 0, \\\"ignore_nonoverlapping_transfrags\\\": \\\"False\\\"}\"}", 
-            "tool_version": "2.2.1.0", 
-            "type": "tool", 
-            "user_outputs": [], 
-            "uuid": "4e1afb8e-9c8b-431f-b25f-75e19e3e95f2"
-        }, 
-        "10": {
-            "annotation": "", 
-            "id": 10, 
-            "input_connections": {
-                "inputA": {
-                    "id": 8, 
-                    "output_name": "outputFile"
-                }, 
-                "inputB": {
-                    "id": 6, 
-                    "output_name": "outputFile"
-                }
-            }, 
-            "inputs": [], 
-            "label": null, 
-            "name": "ClosestBed", 
-            "outputs": [
-                {
-                    "name": "output", 
-                    "type": "bed"
-                }
-            ], 
-            "position": {
-                "left": 1436, 
-                "top": 303
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_closestbed/2.24.0", 
-            "tool_state": "{\"__page__\": 0, \"addition\": \"\\\"True\\\"\", \"k\": \"\\\"1\\\"\", \"inputB\": \"null\", \"mdb\": \"\\\"each\\\"\", \"inputA\": \"null\", \"io\": \"\\\"False\\\"\", \"ties\": \"\\\"all\\\"\", \"addition2\": \"{\\\"fu\\\": \\\"False\\\", \\\"iu\\\": \\\"False\\\", \\\"fd\\\": \\\"False\\\", \\\"__current_case__\\\": 2, \\\"addition2_select\\\": \\\"a\\\", \\\"id\\\": \\\"False\\\"}\", \"chromInfo\": \"\\\"/home/repet_cloud/galaxy/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"strand\": \"\\\"\\\"\"}", 
-            "tool_version": "2.24.0", 
-            "type": "tool", 
-            "user_outputs": [], 
-            "uuid": "9313c43f-34a3-4f5d-bb44-544bfe63de1f"
-        }, 
-        "11": {
-            "annotation": "", 
-            "id": 11, 
-            "input_connections": {
-                "ClassCode|cuffcom_tmap": {
-                    "id": 9, 
-                    "output_name": "input1_tmap"
-                }, 
-                "inputFile": {
-                    "id": 10, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
-            "label": null, 
-            "name": "ClosestToStartSite", 
-            "outputs": [
-                {
-                    "name": "outputFile", 
-                    "type": "bed"
-                }
-            ], 
-            "position": {
-                "left": 1823.5, 
-                "top": 461
-            }, 
-            "post_job_actions": {}, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/teiso/ClosestToStartSite/1.0", 
-            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"ClassCode\": \"{\\\"cuffcom_tmap\\\": null, \\\"get_class_code\\\": \\\"True\\\", \\\"__current_case__\\\": 1}\", \"inputFile\": \"null\"}", 
-            "tool_version": "1.0", 
-            "type": "tool", 
-            "user_outputs": [], 
-            "uuid": "760d9506-a1a6-4a84-81fa-db67ea91ef53"
-        }
-    }, 
-    "uuid": "ad643964-b679-41d0-a74f-e712a8550c7f"
-}
\ No newline at end of file
--- a/TEiso/repository_dependencies.xml	Wed May 25 10:28:25 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-<repositories description="TEiso worflow1 needed repository">
-	<repository changeset_revision="4eb3c3beb9c7" name="tophat2" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu"/>
-	<repository changeset_revision="a1ea9af8d5f4" name="cufflinks" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu"/>
-        <repository changeset_revision="b77178f66fc3" name="cuffcompare" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu"/>
-	<repository changeset_revision="15d6811e6bf5" name="teiso" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu"/>
-	<repository changeset_revision="f8b7dc21b4ee" name="bedtools" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"/>
-</repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Teiso-workflow-final/Galaxy-Workflow-TEiso_workflow.ga	Thu May 26 09:27:07 2016 -0400
@@ -0,0 +1,439 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "TEiso_workflow", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 200
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "a910dd6c-d6e5-4d3a-b3cd-3624c8c509b6"
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 285
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "98cee5d8-d791-4f91-8f29-ccc98003e392"
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 370
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "1fc62c7e-fbb8-48b4-89da-18c629838b7c"
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 455
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "49264998-41ff-4776-81f2-06e3fbaac133"
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Input Dataset"
+                }
+            ], 
+            "label": null, 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 540
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Input Dataset\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": [], 
+            "uuid": "869588d6-af39-40d2-afaa-86a3c9935aa9"
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "refGenomeSource|ownFile": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "singlePaired|input1": {
+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "singlePaired|input2": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "label": null, 
+            "name": "TopHat", 
+            "outputs": [
+                {
+                    "name": "align_summary", 
+                    "type": "txt"
+                }, 
+                {
+                    "name": "fusions", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "insertions", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "deletions", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "junctions", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "accepted_hits", 
+                    "type": "bam"
+                }, 
+                {
+                    "name": "unmapped", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 428, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
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+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Teiso-workflow-final/repository_dependencies.xml	Thu May 26 09:27:07 2016 -0400
@@ -0,0 +1,7 @@
+<repositories description="TEiso worflow1 needed repository">
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+        <repository changeset_revision="b77178f66fc3" name="cuffcompare" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu"/>
+	<repository changeset_revision="775f119b9ac2" name="teiso" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu"/>
+	<repository changeset_revision="f8b7dc21b4ee" name="bedtools" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu"/>
+</repositories>