Mercurial > repos > bgruening > eden_rna_cross_validation_workflow

changeset 0:dd85dc28075f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Thu, 15 May 2014 12:17:52 -0400
parents
children aa4c5b2ec3fd
files EDeN_RNA_Cross_Validation.ga readme.rst repository_dependencies.xml
diffstat 3 files changed, 609 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/EDeN_RNA_Cross_Validation.ga	Thu May 15 12:17:52 2014 -0400
@@ -0,0 +1,564 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "EDeN RNA Cross Validation", 
+    "steps": {
+        "0": {
+            "annotation": "Sequence data (for example piRNA)", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "Sequence data (for example piRNA)", 
+                    "name": "FASTA file"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 192, 
+                "top": 262
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"FASTA file\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {
+                "input": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTA-to-Tabular", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 399, 
+                "top": 200
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "fasta2tab", 
+            "tool_state": "{\"__page__\": 0, \"keep_first\": \"\\\"0\\\"\", \"descr_columns\": \"\\\"1\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/gruening/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "input": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Unique", 
+            "outputs": [
+                {
+                    "name": "outfile", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 445, 
+                "top": 324
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq/0.3", 
+            "tool_state": "{\"__page__\": 0, \"ignore_case\": \"\\\"False\\\"\", \"adv_opts\": \"{\\\"column_end\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"column_start\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}, \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"is_numeric\": \"\\\"False\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/gruening/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "0.3", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "input": {
+                    "id": 2, 
+                    "output_name": "outfile"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Tabular-to-FASTA", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 661, 
+                "top": 336
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutput": {
+                    "action_arguments": {
+                        "newname": "Positive Set"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "output"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "tab2fasta", 
+            "tool_state": "{\"title_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\", \"__page__\": 0, \"seq_col\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"chromInfo\": \"\\\"/home/gruening/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "4": {
+            "annotation": "", 
+            "id": 4, 
+            "input_connections": {
+                "token_set_0|repeat_select|infile": {
+                    "id": 2, 
+                    "output_name": "outfile"
+                }, 
+                "token_set_1|repeat_select|infile": {
+                    "id": 2, 
+                    "output_name": "outfile"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Create text file", 
+            "outputs": [
+                {
+                    "name": "outfile", 
+                    "type": "txt"
+                }
+            ], 
+            "position": {
+                "left": 584.25, 
+                "top": 728.75
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutfile": {
+                    "action_arguments": {
+                        "newname": "target file"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outfile"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/bgruening/recurring_lines/bg_text_file_with_recurring_lines/0.1", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"token_set\": \"[{\\\"__index__\\\": 0, \\\"line\\\": \\\"1\\\", \\\"repeat_select\\\": {\\\"repeat_select_opts\\\": \\\"file\\\", \\\"infile\\\": null, \\\"__current_case__\\\": 1}}, {\\\"__index__\\\": 1, \\\"line\\\": \\\"-1\\\", \\\"repeat_select\\\": {\\\"repeat_select_opts\\\": \\\"file\\\", \\\"infile\\\": null, \\\"__current_case__\\\": 1}}]\"}", 
+            "tool_version": "0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "5": {
+            "annotation": "", 
+            "id": 5, 
+            "input_connections": {
+                "input1": {
+                    "id": 3, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "shuffleseq", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "fasta"
+                }
+            ], 
+            "position": {
+                "left": 675, 
+                "top": 207
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionout_file1": {
+                    "action_arguments": {
+                        "newname": "Negative Set"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/emboss_5/EMBOSS: shuffleseq87/5.0.0", 
+            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"out_format1\": \"\\\"fasta\\\"\", \"__rerun_remap_job_id__\": null, \"shuffle\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/home/gruening/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "5.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "6": {
+            "annotation": "", 
+            "id": 6, 
+            "input_connections": {
+                "input1": {
+                    "id": 3, 
+                    "output_name": "output"
+                }, 
+                "queries_0|input2": {
+                    "id": 5, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Concatenate datasets", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 993, 
+                "top": 246
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "cat1", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"chromInfo\": \"\\\"/home/gruening/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "7": {
+            "annotation": "", 
+            "id": 7, 
+            "input_connections": {
+                "input": {
+                    "id": 6, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "FASTA-to-Tabular", 
+            "outputs": [
+                {
+                    "name": "output", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 259, 
+                "top": 506
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "fasta2tab", 
+            "tool_state": "{\"__page__\": 0, \"keep_first\": \"\\\"0\\\"\", \"descr_columns\": \"\\\"1\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/gruening/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "8": {
+            "annotation": "", 
+            "id": 8, 
+            "input_connections": {
+                "input": {
+                    "id": 7, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Cut", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 455, 
+                "top": 524
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "Cut1", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c2\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/gruening/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "9": {
+            "annotation": "", 
+            "id": 9, 
+            "input_connections": {
+                "input": {
+                    "id": 8, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Add column", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 631, 
+                "top": 463
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "addValue", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"b\\\"\", \"iterate\": \"\\\"no\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/gruening/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "10": {
+            "annotation": "", 
+            "id": 10, 
+            "input_connections": {
+                "input": {
+                    "id": 9, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Add column", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 636, 
+                "top": 567
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "addValue", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"e\\\"\", \"iterate\": \"\\\"no\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/gruening/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "11": {
+            "annotation": "", 
+            "id": 11, 
+            "input_connections": {
+                "input1": {
+                    "id": 10, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Merge Columns", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 802, 
+                "top": 478
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mergeCols1", 
+            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"col2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"1\\\"}\", \"col1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"2\\\"}\", \"chromInfo\": \"\\\"/home/gruening/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"[]\"}", 
+            "tool_version": "1.0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "12": {
+            "annotation": "", 
+            "id": 12, 
+            "input_connections": {
+                "input1": {
+                    "id": 11, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Merge Columns", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 804, 
+                "top": 585
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "mergeCols1", 
+            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"__rerun_remap_job_id__\": null, \"col2\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"3\\\"}\", \"col1\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"4\\\"}\", \"chromInfo\": \"\\\"/home/gruening/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"[]\"}", 
+            "tool_version": "1.0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "13": {
+            "annotation": "", 
+            "id": 13, 
+            "input_connections": {
+                "input": {
+                    "id": 12, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Cut", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 1017, 
+                "top": 453
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "Cut1", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c5\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/gruening/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_version": "1.0.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "14": {
+            "annotation": "", 
+            "id": 14, 
+            "input_connections": {
+                "infile": {
+                    "id": 13, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "EDeN Converters", 
+            "outputs": [
+                {
+                    "name": "outfile", 
+                    "type": "sparsevector"
+                }
+            ], 
+            "position": {
+                "left": 1204, 
+                "top": 453
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "bg_eden_feature", 
+            "tool_state": "{\"smooth_opts\": \"{\\\"smooth_opts_selector\\\": \\\"non_smooth\\\", \\\"__current_case__\\\": 0}\", \"distance\": \"\\\"5\\\"\", \"__page__\": 0, \"hash_bit_size\": \"\\\"15\\\"\", \"__rerun_remap_job_id__\": null, \"no_normalization\": \"\\\"False\\\"\", \"radius\": \"\\\"2\\\"\", \"vertex_degree_threshold\": \"\\\"7\\\"\", \"file_type_opts\": \"{\\\"file_type_opts_selector\\\": \\\"STRINGSEQ\\\", \\\"__current_case__\\\": 3}\", \"graph_type\": \"\\\"DIRECTED\\\"\", \"kernel_type_opts\": \"{\\\"kernel_type_opts_selector\\\": \\\"STRING\\\", \\\"__current_case__\\\": 4}\", \"chromInfo\": \"\\\"/home/gruening/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"infile\": \"null\", \"min_kernel\": \"\\\"False\\\"\"}", 
+            "tool_version": "0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "15": {
+            "annotation": "", 
+            "id": 15, 
+            "input_connections": {
+                "sparse_vector_infile": {
+                    "id": 14, 
+                    "output_name": "outfile"
+                }, 
+                "target_infile": {
+                    "id": 4, 
+                    "output_name": "outfile"
+                }
+            }, 
+            "inputs": [], 
+            "name": "EDeN Crossvalidation", 
+            "outputs": [
+                {
+                    "name": "outfile", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 784, 
+                "top": 734
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "bg_eden_cross_validation", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"sparse_vector_infile\": \"null\", \"target_infile\": \"null\", \"chromInfo\": \"\\\"/home/gruening/projects/code/galaxy-central/tool-data/shared/ucsc/chrom/?.len\\\"\", \"num_cross_validation_folds\": \"\\\"10\\\"\"}", 
+            "tool_version": "0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "16": {
+            "annotation": "", 
+            "id": 16, 
+            "input_connections": {
+                "input": {
+                    "id": 15, 
+                    "output_name": "outfile"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Cut", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 986.25, 
+                "top": 723.75
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "Cut1", 
+            "tool_state": "{\"columnList\": \"\\\"c2,c4\\\"\", \"input\": \"null\", \"delimiter\": \"\\\"T\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
+            "tool_version": "1.0.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "17": {
+            "annotation": "", 
+            "id": 17, 
+            "input_connections": {
+                "infile": {
+                    "id": 16, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Performance metrics", 
+            "outputs": [
+                {
+                    "name": "outfile", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "outfile_plotting", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 1173.75, 
+                "top": 702.75
+            }, 
+            "post_job_actions": {}, 
+            "tool_errors": null, 
+            "tool_id": "testtoolshed.g2.bx.psu.edu/repos/bgruening/perf/stats_perf_tool/5.11.0", 
+            "tool_state": "{\"plot\": \"\\\"-plot roc\\\"\", \"performance_measures\": \"[\\\"-ACC\\\", \\\"-ROC\\\", \\\"-APR\\\"]\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"threshold\": \"\\\"0.0\\\"\", \"infile\": \"null\"}", 
+            "tool_version": "0.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/readme.rst	Thu May 15 12:17:52 2014 -0400
@@ -0,0 +1,38 @@
+This package is a Galaxy workflow for RNA sequence cross validation.
+
+It uses the EDeN suite to train and test on a known set of
+RNA sequences. The negative set of RNA sequences is shuffled
+on the input dataset maintaining composition with shuffleseq (EMBOSS).
+
+See http://www.galaxyproject.org for information about the Galaxy Project.
+
+
+Sample Data
+===========
+
+
+
+Citation
+========
+
+
+
+Availability
+============
+
+This workflow is available on the main Galaxy Tool Shed:
+
+http://toolshed.g2.bx.psu.edu/view/bgruening/eden_rna_cross_validation_workflow
+
+Development is being done on github:
+
+https://github.com/bgruening/galaxytools/workflows/EDeN/
+
+
+Dependencies
+============
+
+These dependencies should be resolved automatically via the Galaxy Tool Shed:
+
+* http://toolshed.g2.bx.psu.edu/view/bgruening/glimmer3
+* http://toolshed.g2.bx.psu.edu/view/devteam/emboss_5
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml	Thu May 15 12:17:52 2014 -0400
@@ -0,0 +1,7 @@
+<?xml version="1.0"?>
+<repositories description="This workflow requires the EDeN suite, EMBOSS and a few small text manipulation tools.">
+    <repository changeset_revision="f034a9d33aca" name="recurring_lines" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="e390b5b6b89c" name="perf" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="5be8af51780d" name="eden_toolbox" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="1b9abd7d2445" name="emboss_5" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+</repositories>