changeset 1:6f95aecbcad1 draft default tip

Uploaded
author bgruening
date Thu, 03 Apr 2014 11:02:03 -0400
parents 3daf197399a2
children
files 1_BAM_file_TO_Heatmap_of_read_coverages.ga 2_BAM_files_TO_clustered_Heatmap_of_read_coverages.ga Add_chr_to_first_column_of_a_6_columns_BED_file.ga Clustered_heatmap_of_signals_around_the_TSSs__1_bigWig_TO_heatmap.ga Compute_and_correct_GC_bias.ga Galaxy-Workflow-1_BAM_file_--_(clustered)_Heatmap_of_read_coverages.ga Galaxy-Workflow-2_BAM_files_--_(clustered)_Heatmap_of_read_coverages.ga Galaxy-Workflow-Add__chr__to_first_column_of_a_BED_file_(must_have_6_columns).ga Galaxy-Workflow-Clustered_heatmap_of_signals_around_the_TSSs.ga Galaxy-Workflow-Compute_and_correct_GC_bias.ga Remove_chr_from_the_beginning_of_genomic_interval_files.ga repository_dependencies.xml
diffstat 12 files changed, 1120 insertions(+), 1052 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/1_BAM_file_TO_Heatmap_of_read_coverages.ga	Thu Apr 03 11:02:03 2014 -0400
@@ -0,0 +1,262 @@
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\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2_BAM_files_TO_clustered_Heatmap_of_read_coverages.ga	Thu Apr 03 11:02:03 2014 -0400
@@ -0,0 +1,293 @@
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+            "tool_state": "{\"__page__\": 0, \"output\": \"{\\\"outFileFormat\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"saveMatrix\\\": \\\"False\\\", \\\"showOutputSettings\\\": \\\"yes\\\", \\\"saveSortedRegions\\\": \\\"False\\\", \\\"__current_case__\\\": 1, \\\"saveData\\\": \\\"False\\\"}\", \"advancedOpt\": \"{\\\"used_multiple_regions\\\": {\\\"clustering\\\": {\\\"k_kmeans\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"clustering_options\\\": \\\"kmeans\\\"}, \\\"used_multiple_regions_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"yAxisLabel\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"xAxisLabel\\\": \\\"\\\", \\\"zMax\\\": \\\"\\\", \\\"heatmapWidth\\\": \\\"7.5\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"zMin\\\": \\\"\\\", \\\"plotTitle\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"averageTypeSummaryPlot\\\": \\\"mean\\\", \\\"whatToShow\\\": \\\"plot, heatmap and colorbar\\\", \\\"missingDataColor\\\": \\\"black\\\", \\\"referencePointLabel\\\": \\\"TSS\\\", \\\"yMin\\\": \\\"\\\", \\\"onePlotPerGroup\\\": \\\"False\\\", \\\"regionsLabel\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"yMax\\\": \\\"\\\", \\\"endLabel\\\": \\\"TES\\\", \\\"sortRegions\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"startLabel\\\": \\\"TSS\\\", \\\"colorMap\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"heatmapHeight\\\": \\\"15.0\\\"}\", \"__rerun_remap_job_id__\": null, \"matrixFile\": \"null\"}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Add_chr_to_first_column_of_a_6_columns_BED_file.ga	Thu Apr 03 11:02:03 2014 -0400
@@ -0,0 +1,145 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "Add 'chr' to first column of a BED file (must have 6 columns)", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "BED file"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 200, 
+                "top": 193
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"BED file\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {
+                "input": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Add column", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 423, 
+                "top": 200
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionout_file1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "addValue", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"chr\\\"\", \"iterate\": \"\\\"no\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\"}", 
+            "tool_version": "1.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "input1": {
+                    "id": 1, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Merge Columns", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 657, 
+                "top": 211
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionout_file1": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "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\\\": \\\"7\\\"}\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\", \"columns\": \"[]\"}", 
+            "tool_version": "1.0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "input": {
+                    "id": 2, 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Cut", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 872, 
+                "top": 205
+            }, 
+            "post_job_actions": {
+                "ChangeDatatypeActionout_file1": {
+                    "action_arguments": {
+                        "newtype": "interval"
+                    }, 
+                    "action_type": "ChangeDatatypeAction", 
+                    "output_name": "out_file1"
+                }, 
+                "RenameDatasetActionout_file1": {
+                    "action_arguments": {
+                        "newname": "added \"chr\" to chromosome name"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "Cut1", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c8,c2,c3,c4,c5,c6\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\"}", 
+            "tool_version": "1.0.2", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Clustered_heatmap_of_signals_around_the_TSSs__1_bigWig_TO_heatmap.ga	Thu Apr 03 11:02:03 2014 -0400
@@ -0,0 +1,205 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "Clustered heatmap of signals around the TSSs (1 bigWig --> heatmap)", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "Genes"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 175, 
+                "top": 186.5
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"Genes\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "score file"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 168, 
+                "top": 304.5
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"score file\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "regionsFiles_0|regionsFile": {
+                    "id": 0, 
+                    "output_name": "output"
+                }, 
+                "scoreFile": {
+                    "id": 1, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool computeMatrix", 
+                    "name": "mode"
+                }, 
+                {
+                    "description": "runtime parameter for tool computeMatrix", 
+                    "name": "mode"
+                }
+            ], 
+            "name": "computeMatrix", 
+            "outputs": [
+                {
+                    "name": "outFileName", 
+                    "type": "bgzip"
+                }, 
+                {
+                    "name": "outFileNameData", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "outFileSortedRegions", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "outFileNameMatrix", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 490.6166687011719, 
+                "top": 485.11669921875
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutFileNameData": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "outFileNameData"
+                }, 
+                "HideDatasetActionoutFileNameMatrix": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "outFileNameMatrix"
+                }, 
+                "HideDatasetActionoutFileSortedRegions": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "outFileSortedRegions"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeMatrix/1.1.0", 
+            "tool_state": "{\"__page__\": 0, \"scoreFile\": \"null\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"afterRegionStartLength\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"beforeRegionStartLength\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"nanAfterEnd\\\": \\\"False\\\", \\\"__current_case__\\\": 1, \\\"referencePoint\\\": \\\"TSS\\\", \\\"mode_select\\\": \\\"reference-point\\\"}\", \"output\": \"{\\\"saveMatrix\\\": \\\"False\\\", \\\"saveSortedRegions\\\": \\\"True\\\", \\\"showOutputSettings\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"saveData\\\": \\\"False\\\"}\", \"advancedOpt\": \"{\\\"averageTypeBins\\\": \\\"mean\\\", \\\"maxThreshold\\\": \\\"\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"skipZeros\\\": \\\"True\\\", \\\"binSize\\\": \\\"50\\\", \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"scale\\\": \\\"\\\", \\\"__current_case__\\\": 1, \\\"minThreshold\\\": \\\"\\\", \\\"sortRegions\\\": \\\"no\\\", \\\"missingDataAsZero\\\": \\\"True\\\"}\", \"regionsFiles\": \"[{\\\"__index__\\\": 0, \\\"regionsFile\\\": null, \\\"label\\\": \\\"Genes\\\"}]\"}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "3": {
+            "annotation": "", 
+            "id": 3, 
+            "input_connections": {
+                "matrixFile": {
+                    "id": 2, 
+                    "output_name": "outFileName"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool heatmapper", 
+                    "name": "output"
+                }, 
+                {
+                    "description": "runtime parameter for tool heatmapper", 
+                    "name": "advancedOpt"
+                }, 
+                {
+                    "description": "runtime parameter for tool heatmapper", 
+                    "name": "advancedOpt"
+                }, 
+                {
+                    "description": "runtime parameter for tool heatmapper", 
+                    "name": "advancedOpt"
+                }
+            ], 
+            "name": "heatmapper", 
+            "outputs": [
+                {
+                    "name": "outFileName", 
+                    "type": "png"
+                }, 
+                {
+                    "name": "outFileNameData", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "outFileSortedRegions", 
+                    "type": "bed"
+                }, 
+                {
+                    "name": "outFileNameMatrix", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 834, 
+                "top": 487.5
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutFileNameData": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "outFileNameData"
+                }, 
+                "HideDatasetActionoutFileNameMatrix": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "outFileNameMatrix"
+                }, 
+                "HideDatasetActionoutFileSortedRegions": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "outFileSortedRegions"
+                }, 
+                "RenameDatasetActionoutFileName": {
+                    "action_arguments": {
+                        "newname": "Heatmap of scores around the TSS"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outFileName"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_heatmapper/1.1.0", 
+            "tool_state": "{\"__page__\": 0, \"output\": \"{\\\"outFileFormat\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"saveMatrix\\\": \\\"False\\\", \\\"showOutputSettings\\\": \\\"yes\\\", \\\"saveSortedRegions\\\": \\\"False\\\", \\\"__current_case__\\\": 1, \\\"saveData\\\": \\\"False\\\"}\", \"advancedOpt\": \"{\\\"used_multiple_regions\\\": {\\\"clustering\\\": {\\\"k_kmeans\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"clustering_options\\\": \\\"kmeans\\\"}, \\\"used_multiple_regions_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"yAxisLabel\\\": \\\"genes\\\", \\\"xAxisLabel\\\": \\\"distance from TSS (bp)\\\", \\\"zMax\\\": \\\"\\\", \\\"heatmapWidth\\\": \\\"7.5\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"zMin\\\": \\\"\\\", \\\"plotTitle\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"averageTypeSummaryPlot\\\": \\\"mean\\\", \\\"whatToShow\\\": \\\"plot, heatmap and colorbar\\\", \\\"missingDataColor\\\": \\\"black\\\", \\\"referencePointLabel\\\": \\\"TSS\\\", \\\"yMin\\\": \\\"\\\", \\\"onePlotPerGroup\\\": \\\"False\\\", \\\"regionsLabel\\\": \\\"genes\\\", \\\"yMax\\\": \\\"\\\", \\\"endLabel\\\": \\\"TES\\\", \\\"sortRegions\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"startLabel\\\": \\\"TSS\\\", \\\"colorMap\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"heatmapHeight\\\": \\\"15.0\\\"}\", \"__rerun_remap_job_id__\": null, \"matrixFile\": \"null\"}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Compute_and_correct_GC_bias.ga	Thu Apr 03 11:02:03 2014 -0400
@@ -0,0 +1,145 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "Compute and correct GC bias", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "BAM file to be checked for GC bias"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 148, 
+                "top": 505.88330078125
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"BAM file to be checked for GC bias\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {
+                "bamInput": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool computeGCBias", 
+                    "name": "region"
+                }, 
+                {
+                    "description": "runtime parameter for tool computeGCBias", 
+                    "name": "source"
+                }, 
+                {
+                    "description": "runtime parameter for tool computeGCBias", 
+                    "name": "effectiveGenomeSize"
+                }, 
+                {
+                    "description": "runtime parameter for tool computeGCBias", 
+                    "name": "image_format"
+                }, 
+                {
+                    "description": "runtime parameter for tool computeGCBias", 
+                    "name": "fragmentLength"
+                }
+            ], 
+            "name": "computeGCBias", 
+            "outputs": [
+                {
+                    "name": "outFileName", 
+                    "type": "tabular"
+                }, 
+                {
+                    "name": "outImageName", 
+                    "type": "png"
+                }
+            ], 
+            "position": {
+                "left": 404.61669921875, 
+                "top": 200
+            }, 
+            "post_job_actions": {
+                "HideDatasetActionoutFileName": {
+                    "action_arguments": {}, 
+                    "action_type": "HideDatasetAction", 
+                    "output_name": "outFileName"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeGCBias/1.1.0", 
+            "tool_state": "{\"__page__\": 0, \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bamInput\": \"null\", \"source\": \"{\\\"input1_2bit\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"ref_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"effectiveGenomeSize\": \"{\\\"effectiveGenomeSize_opt\\\": \\\"specific\\\", \\\"effectiveGenomeSize\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"advancedOpt\": \"{\\\"filterOut\\\": null, \\\"extraSampling\\\": null, \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"sampleSize\\\": \\\"50000000\\\", \\\"__current_case__\\\": 1, \\\"regionSize\\\": \\\"300\\\"}\", \"image_format\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fragmentLength\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }, 
+        "2": {
+            "annotation": "", 
+            "id": 2, 
+            "input_connections": {
+                "GCbiasFrequenciesFile": {
+                    "id": 1, 
+                    "output_name": "outFileName"
+                }, 
+                "bamInput": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool correctGCBias", 
+                    "name": "region"
+                }, 
+                {
+                    "description": "runtime parameter for tool correctGCBias", 
+                    "name": "source"
+                }, 
+                {
+                    "description": "runtime parameter for tool correctGCBias", 
+                    "name": "effectiveGenomeSize"
+                }
+            ], 
+            "name": "correctGCBias", 
+            "outputs": [
+                {
+                    "name": "outFileName", 
+                    "type": "bam"
+                }
+            ], 
+            "position": {
+                "left": 734.61669921875, 
+                "top": 462
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionoutFileName": {
+                    "action_arguments": {
+                        "newname": "GCcorrected BAM file"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "outFileName"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_correctGCBias/1.1.0", 
+            "tool_state": "{\"__page__\": 0, \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bamInput\": \"null\", \"source\": \"{\\\"input1_2bit\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"ref_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"effectiveGenomeSize\": \"{\\\"effectiveGenomeSize_opt\\\": \\\"specific\\\", \\\"effectiveGenomeSize\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"GCbiasFrequenciesFile\": \"null\", \"advancedOpt\": \"{\\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"binSize\\\": \\\"50\\\"}\", \"__rerun_remap_job_id__\": null}", 
+            "tool_version": "1.1.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- a/Galaxy-Workflow-1_BAM_file_--_(clustered)_Heatmap_of_read_coverages.ga	Tue Feb 04 13:46:24 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,262 +0,0 @@
-{
-    "a_galaxy_workflow": "true", 
-    "annotation": "1 BAM file from D.melanogaster will be normalized to 1x sequencing depth and a heatmap can be generated for a user-specified BED file (with genes being scaled to a length of 1.5kb)", 
-    "format-version": "0.1", 
-    "name": "1 BAM file -->(clustered) Heatmap of read coverages", 
-    "steps": {
-        "0": {
-            "annotation": "sorted BAM file, e.g. Input from Data Library", 
-            "id": 0, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "sorted BAM file, e.g. Input from Data Library", 
-                    "name": "file of mapped reads"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 257.5, 
-                "top": 480
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"file of mapped reads\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "1": {
-            "annotation": "BED or INTERVAL file of genome regions to plot the read coverage for", 
-            "id": 1, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "BED or INTERVAL file of genome regions to plot the read coverage for", 
-                    "name": "regions"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 583.5, 
-                "top": 234
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"regions\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "2": {
-            "annotation": "this will generate a coverage file normalized to 1x sequencing depth (for D.melanogaster!)", 
-            "id": 2, 
-            "input_connections": {
-                "bamInput": {
-                    "id": 0, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool bamCoverage", 
-                    "name": "region"
-                }, 
-                {
-                    "description": "runtime parameter for tool bamCoverage", 
-                    "name": "fragmentLength"
-                }
-            ], 
-            "name": "bamCoverage", 
-            "outputs": [
-                {
-                    "name": "outFileName", 
-                    "type": "bigwig"
-                }
-            ], 
-            "position": {
-                "left": 491.6166687011719, 
-                "top": 474.11669921875
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-            "post_job_actions": {
-                "HideDatasetActionoutFileName": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileName"
-                }, 
-                "RenameDatasetActionoutFileName": {
-                    "action_arguments": {
-                        "newname": "Drosophila coverage file"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outFileName"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_bamCoverage/1.0.4", 
-            "tool_state": "{\"__page__\": 0, \"outFileFormat\": \"\\\"bigwig\\\"\", \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bamInput\": \"null\", \"binSize\": \"\\\"50\\\"\", \"scaling\": \"{\\\"effectiveGenomeSize\\\": {\\\"effectiveGenomeSize_opt\\\": \\\"121400000\\\", \\\"__current_case__\\\": 3}, \\\"type\\\": \\\"1x\\\", \\\"__current_case__\\\": 2}\", \"__rerun_remap_job_id__\": null, \"advancedOpt\": \"{\\\"ignoreDuplicates\\\": \\\"True\\\", \\\"doNotExtendPairedEnds\\\": \\\"False\\\", \\\"smoothLength\\\": \\\"150\\\", \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"minMappingQuality\\\": \\\"10\\\"}\", \"fragmentLength\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
-            "tool_version": "1.0.4", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "3": {
-            "annotation": "", 
-            "id": 3, 
-            "input_connections": {
-                "regionsFiles_0|regionsFile": {
-                    "id": 1, 
-                    "output_name": "output"
-                }, 
-                "scoreFile": {
-                    "id": 2, 
-                    "output_name": "outFileName"
-                }
-            }, 
-            "inputs": [], 
-            "name": "computeMatrix", 
-            "outputs": [
-                {
-                    "name": "outFileName", 
-                    "type": "bgzip"
-                }, 
-                {
-                    "name": "outFileNameData", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "outFileSortedRegions", 
-                    "type": "bed"
-                }, 
-                {
-                    "name": "outFileNameMatrix", 
-                    "type": "tabular"
-                }
-            ], 
-            "position": {
-                "left": 828.6166687011719, 
-                "top": 358.1166687011719
-            }, 
-            "post_job_actions": {
-                "HideDatasetActionoutFileNameData": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileNameData"
-                }, 
-                "HideDatasetActionoutFileNameMatrix": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileNameMatrix"
-                }, 
-                "HideDatasetActionoutFileSortedRegions": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileSortedRegions"
-                }, 
-                "RenameDatasetActionoutFileName": {
-                    "action_arguments": {
-                        "newname": "computeMatrix: matrix of coverage values for BED file"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outFileName"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeMatrix/1.0.4", 
-            "tool_state": "{\"__page__\": 0, \"scoreFile\": \"null\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"startLabel\\\": \\\"TSS\\\", \\\"regionStartLength\\\": {\\\"afterRegionStartLength\\\": \\\"1000\\\", \\\"regionStartLength_select\\\": \\\"yes\\\", \\\"beforeRegionStartLength\\\": \\\"1000\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"endLabel\\\": \\\"TES\\\", \\\"regionBodyLength\\\": \\\"2000\\\", \\\"mode_select\\\": \\\"scale-regions\\\"}\", \"output\": \"{\\\"showOutputSettings\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"advancedOpt\": \"{\\\"averageTypeBins\\\": \\\"mean\\\", \\\"maxThreshold\\\": \\\"\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"skipZeros\\\": \\\"True\\\", \\\"binSize\\\": \\\"50\\\", \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"scale\\\": \\\"\\\", \\\"__current_case__\\\": 1, \\\"minThreshold\\\": \\\"\\\", \\\"sortRegions\\\": \\\"no\\\", \\\"missingDataAsZero\\\": \\\"True\\\"}\", \"regionsFiles\": \"[{\\\"__index__\\\": 0, \\\"regionsFile\\\": null, \\\"label\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\"}", 
-            "tool_version": "1.0.4", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "4": {
-            "annotation": "create a heatmap, if wanted, kmeans clustering can be performed", 
-            "id": 4, 
-            "input_connections": {
-                "matrixFile": {
-                    "id": 3, 
-                    "output_name": "outFileName"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "output"
-                }, 
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "advancedOpt"
-                }, 
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "advancedOpt"
-                }, 
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "advancedOpt"
-                }, 
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "advancedOpt"
-                }, 
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "advancedOpt"
-                }
-            ], 
-            "name": "heatmapper", 
-            "outputs": [
-                {
-                    "name": "outFileName", 
-                    "type": "png"
-                }, 
-                {
-                    "name": "outFileNameData", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "outFileSortedRegions", 
-                    "type": "bed"
-                }, 
-                {
-                    "name": "outFileNameMatrix", 
-                    "type": "tabular"
-                }
-            ], 
-            "position": {
-                "left": 1139.5, 
-                "top": 392
-            }, 
-            "post_job_actions": {
-                "HideDatasetActionoutFileNameData": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileNameData"
-                }, 
-                "HideDatasetActionoutFileNameMatrix": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileNameMatrix"
-                }, 
-                "HideDatasetActionoutFileSortedRegions": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileSortedRegions"
-                }, 
-                "RenameDatasetActionoutFileName": {
-                    "action_arguments": {
-                        "newname": "Heatmap of treatment_control_log2ratios"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outFileName"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_heatmapper/1.0.4", 
-            "tool_state": "{\"__page__\": 0, \"output\": \"{\\\"outFileFormat\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"saveMatrix\\\": \\\"False\\\", \\\"showOutputSettings\\\": \\\"yes\\\", \\\"saveSortedRegions\\\": \\\"False\\\", \\\"__current_case__\\\": 1, \\\"saveData\\\": \\\"False\\\"}\", \"advancedOpt\": \"{\\\"used_multiple_regions\\\": {\\\"clustering\\\": {\\\"k_kmeans\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"clustering_options\\\": \\\"kmeans\\\"}, \\\"used_multiple_regions_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"yAxisLabel\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"xAxisLabel\\\": \\\"\\\", \\\"zMax\\\": \\\"\\\", \\\"heatmapWidth\\\": \\\"7.5\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"zMin\\\": \\\"\\\", \\\"plotTitle\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"averageTypeSummaryPlot\\\": \\\"mean\\\", \\\"whatToShow\\\": \\\"plot, heatmap and colorbar\\\", \\\"missingDataColor\\\": \\\"black\\\", \\\"referencePointLabel\\\": \\\"TSS\\\", \\\"yMin\\\": \\\"\\\", \\\"onePlotPerGroup\\\": \\\"False\\\", \\\"regionsLabel\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"yMax\\\": \\\"\\\", \\\"endLabel\\\": \\\"TES\\\", \\\"sortRegions\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"startLabel\\\": \\\"TSS\\\", \\\"colorMap\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"heatmapHeight\\\": \\\"15.0\\\"}\", \"__rerun_remap_job_id__\": null, \"matrixFile\": \"null\"}", 
-            "tool_version": "1.0.4", 
-            "type": "tool", 
-            "user_outputs": []
-        }
-    }
-}
--- a/Galaxy-Workflow-2_BAM_files_--_(clustered)_Heatmap_of_read_coverages.ga	Tue Feb 04 13:46:24 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,293 +0,0 @@
-{
-    "a_galaxy_workflow": "true", 
-    "annotation": "Normalizes 2 BAM files to each other (log2ratio of BAM-file 1 /  BAM file 2). Then generates a heatmap for regions supplied in 1 BED file (clustering possible). Output: bigWig file, computeMatrix table, heatmapper image", 
-    "format-version": "0.1", 
-    "name": "2 BAM files -->(clustered) Heatmap of read coverages", 
-    "steps": {
-        "0": {
-            "annotation": "sorted BAM file", 
-            "id": 0, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "sorted BAM file", 
-                    "name": "file 1 of mapped reads, e.g. treated sample"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 257.5, 
-                "top": 480
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"file 1 of mapped reads, e.g. treated sample\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "1": {
-            "annotation": "BED or INTERVAL file of genome regions to plot the read coverage for", 
-            "id": 1, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "BED or INTERVAL file of genome regions to plot the read coverage for", 
-                    "name": "regions"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 590.5, 
-                "top": 239
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"regions\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "2": {
-            "annotation": "sorted BAM file", 
-            "id": 2, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "sorted BAM file", 
-                    "name": "file 2 of mapped reads, e.g. control sample"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 276.5, 
-                "top": 594.5
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"file 2 of mapped reads, e.g. control sample\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "3": {
-            "annotation": "generates a normalized coverage file (bigWig format)", 
-            "id": 3, 
-            "input_connections": {
-                "bamFile1": {
-                    "id": 0, 
-                    "output_name": "output"
-                }, 
-                "bamFile2": {
-                    "id": 2, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool bamCompare", 
-                    "name": "region"
-                }, 
-                {
-                    "description": "runtime parameter for tool bamCompare", 
-                    "name": "advancedOpt"
-                }, 
-                {
-                    "description": "runtime parameter for tool bamCompare", 
-                    "name": "fragmentLength"
-                }
-            ], 
-            "name": "bamCompare", 
-            "outputs": [
-                {
-                    "name": "outFileName", 
-                    "type": "bigwig"
-                }
-            ], 
-            "position": {
-                "left": 476.5, 
-                "top": 486.5
-            }, 
-            "post_job_actions": {
-                "HideDatasetActionoutFileName": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileName"
-                }, 
-                "RenameDatasetActionoutFileName": {
-                    "action_arguments": {
-                        "newname": "BAM1_vs_BAM2_log2ratio.bigwig"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outFileName"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_bamCompare/1.0.4", 
-            "tool_state": "{\"comparison\": \"{\\\"type\\\": \\\"log2\\\", \\\"__current_case__\\\": 0}\", \"bamFile2\": \"null\", \"outFileFormat\": \"\\\"bigwig\\\"\", \"bamFile1\": \"null\", \"__page__\": 0, \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"binSize\": \"\\\"50\\\"\", \"scaling\": \"{\\\"method\\\": \\\"readCount\\\", \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"advancedOpt\": \"{\\\"ignoreDuplicates\\\": \\\"True\\\", \\\"ignoreForNormalization\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"doNotExtendPairedEnds\\\": \\\"False\\\", \\\"missingDataAsZero\\\": \\\"True\\\", \\\"smoothLength\\\": \\\"150\\\", \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"minMappingQuality\\\": \\\"10\\\"}\", \"fragmentLength\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
-            "tool_version": "1.0.4", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "4": {
-            "annotation": "", 
-            "id": 4, 
-            "input_connections": {
-                "regionsFiles_0|regionsFile": {
-                    "id": 1, 
-                    "output_name": "output"
-                }, 
-                "scoreFile": {
-                    "id": 3, 
-                    "output_name": "outFileName"
-                }
-            }, 
-            "inputs": [], 
-            "name": "computeMatrix", 
-            "outputs": [
-                {
-                    "name": "outFileName", 
-                    "type": "bgzip"
-                }, 
-                {
-                    "name": "outFileNameData", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "outFileSortedRegions", 
-                    "type": "bed"
-                }, 
-                {
-                    "name": "outFileNameMatrix", 
-                    "type": "tabular"
-                }
-            ], 
-            "position": {
-                "left": 835.61669921875, 
-                "top": 364.1166687011719
-            }, 
-            "post_job_actions": {
-                "HideDatasetActionoutFileNameData": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileNameData"
-                }, 
-                "HideDatasetActionoutFileNameMatrix": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileNameMatrix"
-                }, 
-                "HideDatasetActionoutFileSortedRegions": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileSortedRegions"
-                }, 
-                "RenameDatasetActionoutFileName": {
-                    "action_arguments": {
-                        "newname": "computeMatrix: matrix of coverage values for BED file"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outFileName"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeMatrix/1.0.4", 
-            "tool_state": "{\"__page__\": 0, \"scoreFile\": \"null\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"startLabel\\\": \\\"TSS\\\", \\\"regionStartLength\\\": {\\\"afterRegionStartLength\\\": \\\"1000\\\", \\\"regionStartLength_select\\\": \\\"yes\\\", \\\"beforeRegionStartLength\\\": \\\"1000\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0, \\\"endLabel\\\": \\\"TES\\\", \\\"regionBodyLength\\\": \\\"2000\\\", \\\"mode_select\\\": \\\"scale-regions\\\"}\", \"output\": \"{\\\"showOutputSettings\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"advancedOpt\": \"{\\\"averageTypeBins\\\": \\\"mean\\\", \\\"maxThreshold\\\": \\\"\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"skipZeros\\\": \\\"True\\\", \\\"binSize\\\": \\\"50\\\", \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"scale\\\": \\\"\\\", \\\"__current_case__\\\": 1, \\\"minThreshold\\\": \\\"\\\", \\\"sortRegions\\\": \\\"no\\\", \\\"missingDataAsZero\\\": \\\"True\\\"}\", \"regionsFiles\": \"[{\\\"__index__\\\": 0, \\\"regionsFile\\\": null, \\\"label\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\"}", 
-            "tool_version": "1.0.4", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "5": {
-            "annotation": "create a heatmap, if wanted, kmeans clustering can be performed", 
-            "id": 5, 
-            "input_connections": {
-                "matrixFile": {
-                    "id": 4, 
-                    "output_name": "outFileName"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "output"
-                }, 
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "advancedOpt"
-                }, 
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "advancedOpt"
-                }, 
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "advancedOpt"
-                }, 
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "advancedOpt"
-                }, 
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "advancedOpt"
-                }
-            ], 
-            "name": "heatmapper", 
-            "outputs": [
-                {
-                    "name": "outFileName", 
-                    "type": "png"
-                }, 
-                {
-                    "name": "outFileNameData", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "outFileSortedRegions", 
-                    "type": "bed"
-                }, 
-                {
-                    "name": "outFileNameMatrix", 
-                    "type": "tabular"
-                }
-            ], 
-            "position": {
-                "left": 1144.5, 
-                "top": 397
-            }, 
-            "post_job_actions": {
-                "HideDatasetActionoutFileNameData": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileNameData"
-                }, 
-                "HideDatasetActionoutFileNameMatrix": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileNameMatrix"
-                }, 
-                "HideDatasetActionoutFileSortedRegions": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileSortedRegions"
-                }, 
-                "RenameDatasetActionoutFileName": {
-                    "action_arguments": {
-                        "newname": "Heatmap of treatment_control_log2ratios"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outFileName"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_heatmapper/1.0.4", 
-            "tool_state": "{\"__page__\": 0, \"output\": \"{\\\"outFileFormat\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"saveMatrix\\\": \\\"False\\\", \\\"showOutputSettings\\\": \\\"yes\\\", \\\"saveSortedRegions\\\": \\\"False\\\", \\\"__current_case__\\\": 1, \\\"saveData\\\": \\\"False\\\"}\", \"advancedOpt\": \"{\\\"used_multiple_regions\\\": {\\\"clustering\\\": {\\\"k_kmeans\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"clustering_options\\\": \\\"kmeans\\\"}, \\\"used_multiple_regions_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"yAxisLabel\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"xAxisLabel\\\": \\\"\\\", \\\"zMax\\\": \\\"\\\", \\\"heatmapWidth\\\": \\\"7.5\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"zMin\\\": \\\"\\\", \\\"plotTitle\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"averageTypeSummaryPlot\\\": \\\"mean\\\", \\\"whatToShow\\\": \\\"plot, heatmap and colorbar\\\", \\\"missingDataColor\\\": \\\"black\\\", \\\"referencePointLabel\\\": \\\"TSS\\\", \\\"yMin\\\": \\\"\\\", \\\"onePlotPerGroup\\\": \\\"False\\\", \\\"regionsLabel\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"yMax\\\": \\\"\\\", \\\"endLabel\\\": \\\"TES\\\", \\\"sortRegions\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"startLabel\\\": \\\"TSS\\\", \\\"colorMap\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"heatmapHeight\\\": \\\"15.0\\\"}\", \"__rerun_remap_job_id__\": null, \"matrixFile\": \"null\"}", 
-            "tool_version": "1.0.4", 
-            "type": "tool", 
-            "user_outputs": []
-        }
-    }
-}
\ No newline at end of file
--- a/Galaxy-Workflow-Add__chr__to_first_column_of_a_BED_file_(must_have_6_columns).ga	Tue Feb 04 13:46:24 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,145 +0,0 @@
-{
-    "a_galaxy_workflow": "true", 
-    "annotation": "", 
-    "format-version": "0.1", 
-    "name": "Add 'chr' to first column of a BED file (must have 6 columns)", 
-    "steps": {
-        "0": {
-            "annotation": "The BED file MUST have 6 columns. Otherwise this workflow will fail.", 
-            "id": 0, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "The BED file MUST have 6 columns. Otherwise this workflow will fail.", 
-                    "name": "BED file"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 200, 
-                "top": 193
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"BED file\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "1": {
-            "annotation": "", 
-            "id": 1, 
-            "input_connections": {
-                "input": {
-                    "id": 0, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Add column", 
-            "outputs": [
-                {
-                    "name": "out_file1", 
-                    "type": "input"
-                }
-            ], 
-            "position": {
-                "left": 423, 
-                "top": 200
-            }, 
-            "post_job_actions": {
-                "HideDatasetActionout_file1": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "addValue", 
-            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"exp\": \"\\\"chr\\\"\", \"iterate\": \"\\\"no\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\"}", 
-            "tool_version": "1.0.0", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "2": {
-            "annotation": "", 
-            "id": 2, 
-            "input_connections": {
-                "input1": {
-                    "id": 1, 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Merge Columns", 
-            "outputs": [
-                {
-                    "name": "out_file1", 
-                    "type": "tabular"
-                }
-            ], 
-            "position": {
-                "left": 657, 
-                "top": 211
-            }, 
-            "post_job_actions": {
-                "HideDatasetActionout_file1": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "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\\\": \\\"7\\\"}\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\", \"columns\": \"[]\"}", 
-            "tool_version": "1.0.1", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "3": {
-            "annotation": "", 
-            "id": 3, 
-            "input_connections": {
-                "input": {
-                    "id": 2, 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "inputs": [], 
-            "name": "Cut", 
-            "outputs": [
-                {
-                    "name": "out_file1", 
-                    "type": "tabular"
-                }
-            ], 
-            "position": {
-                "left": 872, 
-                "top": 205
-            }, 
-            "post_job_actions": {
-                "ChangeDatatypeActionout_file1": {
-                    "action_arguments": {
-                        "newtype": "interval"
-                    }, 
-                    "action_type": "ChangeDatatypeAction", 
-                    "output_name": "out_file1"
-                }, 
-                "RenameDatasetActionout_file1": {
-                    "action_arguments": {
-                        "newname": "added \"chr\" to chromosome name"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "out_file1"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "Cut1", 
-            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"delimiter\": \"\\\"T\\\"\", \"columnList\": \"\\\"c8,c2,c3,c4,c5,c6\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\"}", 
-            "tool_version": "1.0.2", 
-            "type": "tool", 
-            "user_outputs": []
-        }
-    }
-}
\ No newline at end of file
--- a/Galaxy-Workflow-Clustered_heatmap_of_signals_around_the_TSSs.ga	Tue Feb 04 13:46:24 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,205 +0,0 @@
-{
-    "a_galaxy_workflow": "true", 
-    "annotation": "1 bigWig, 1 \nBED --> clustered heatmap", 
-    "format-version": "0.1", 
-    "name": "Clustered heatmap of signals around the TSSs", 
-    "steps": {
-        "0": {
-            "annotation": "Gene list must:\na) match the genome of the score file\nb) be in INTERVAL or BED format with the STRAND being specified", 
-            "id": 0, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "Gene list must:\na) match the genome of the score file\nb) be in INTERVAL or BED format with the STRAND being specified", 
-                    "name": "Genes"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 175, 
-                "top": 186.5
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"Genes\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "1": {
-            "annotation": "must be in bigWig format, score can be anything: read coverages, GC content...", 
-            "id": 1, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "must be in bigWig format, score can be anything: read coverages, GC content...", 
-                    "name": "score file"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 168, 
-                "top": 304.5
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"score file\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "2": {
-            "annotation": "computes the matrix for the heatmap", 
-            "id": 2, 
-            "input_connections": {
-                "regionsFiles_0|regionsFile": {
-                    "id": 0, 
-                    "output_name": "output"
-                }, 
-                "scoreFile": {
-                    "id": 1, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool computeMatrix", 
-                    "name": "mode"
-                }, 
-                {
-                    "description": "runtime parameter for tool computeMatrix", 
-                    "name": "mode"
-                }
-            ], 
-            "name": "computeMatrix", 
-            "outputs": [
-                {
-                    "name": "outFileName", 
-                    "type": "bgzip"
-                }, 
-                {
-                    "name": "outFileNameData", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "outFileSortedRegions", 
-                    "type": "bed"
-                }, 
-                {
-                    "name": "outFileNameMatrix", 
-                    "type": "tabular"
-                }
-            ], 
-            "position": {
-                "left": 490.6166687011719, 
-                "top": 485.11669921875
-            }, 
-            "post_job_actions": {
-                "HideDatasetActionoutFileNameData": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileNameData"
-                }, 
-                "HideDatasetActionoutFileNameMatrix": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileNameMatrix"
-                }, 
-                "HideDatasetActionoutFileSortedRegions": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileSortedRegions"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeMatrix/1.0.3", 
-            "tool_state": "{\"__page__\": 0, \"scoreFile\": \"null\", \"__rerun_remap_job_id__\": null, \"mode\": \"{\\\"afterRegionStartLength\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"beforeRegionStartLength\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"nanAfterEnd\\\": \\\"False\\\", \\\"__current_case__\\\": 1, \\\"referencePoint\\\": \\\"TSS\\\", \\\"mode_select\\\": \\\"reference-point\\\"}\", \"output\": \"{\\\"saveMatrix\\\": \\\"False\\\", \\\"saveSortedRegions\\\": \\\"True\\\", \\\"showOutputSettings\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"saveData\\\": \\\"False\\\"}\", \"advancedOpt\": \"{\\\"averageTypeBins\\\": \\\"mean\\\", \\\"maxThreshold\\\": \\\"\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"skipZeros\\\": \\\"True\\\", \\\"binSize\\\": \\\"50\\\", \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"scale\\\": \\\"\\\", \\\"__current_case__\\\": 1, \\\"minThreshold\\\": \\\"\\\", \\\"sortRegions\\\": \\\"no\\\", \\\"missingDataAsZero\\\": \\\"True\\\"}\", \"regionsFiles\": \"[{\\\"__index__\\\": 0, \\\"regionsFile\\\": null, \\\"label\\\": \\\"Genes\\\"}]\"}", 
-            "tool_version": "1.0.3", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "3": {
-            "annotation": "", 
-            "id": 3, 
-            "input_connections": {
-                "matrixFile": {
-                    "id": 2, 
-                    "output_name": "outFileName"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "output"
-                }, 
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "advancedOpt"
-                }, 
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "advancedOpt"
-                }, 
-                {
-                    "description": "runtime parameter for tool heatmapper", 
-                    "name": "advancedOpt"
-                }
-            ], 
-            "name": "heatmapper", 
-            "outputs": [
-                {
-                    "name": "outFileName", 
-                    "type": "png"
-                }, 
-                {
-                    "name": "outFileNameData", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "outFileSortedRegions", 
-                    "type": "bed"
-                }, 
-                {
-                    "name": "outFileNameMatrix", 
-                    "type": "tabular"
-                }
-            ], 
-            "position": {
-                "left": 834, 
-                "top": 487.5
-            }, 
-            "post_job_actions": {
-                "HideDatasetActionoutFileNameData": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileNameData"
-                }, 
-                "HideDatasetActionoutFileNameMatrix": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileNameMatrix"
-                }, 
-                "HideDatasetActionoutFileSortedRegions": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileSortedRegions"
-                }, 
-                "RenameDatasetActionoutFileName": {
-                    "action_arguments": {
-                        "newname": "Heatmap of scores around the TSS"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outFileName"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_heatmapper/1.0.3", 
-            "tool_state": "{\"__page__\": 0, \"output\": \"{\\\"outFileFormat\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"saveMatrix\\\": \\\"False\\\", \\\"showOutputSettings\\\": \\\"yes\\\", \\\"saveSortedRegions\\\": \\\"False\\\", \\\"__current_case__\\\": 1, \\\"saveData\\\": \\\"False\\\"}\", \"advancedOpt\": \"{\\\"used_multiple_regions\\\": {\\\"clustering\\\": {\\\"k_kmeans\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"clustering_options\\\": \\\"kmeans\\\"}, \\\"used_multiple_regions_options\\\": \\\"no\\\", \\\"__current_case__\\\": 0}, \\\"yAxisLabel\\\": \\\"genes\\\", \\\"xAxisLabel\\\": \\\"distance from TSS (bp)\\\", \\\"zMax\\\": \\\"\\\", \\\"heatmapWidth\\\": \\\"7.5\\\", \\\"sortUsing\\\": \\\"mean\\\", \\\"zMin\\\": \\\"\\\", \\\"plotTitle\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"averageTypeSummaryPlot\\\": \\\"mean\\\", \\\"whatToShow\\\": \\\"plot, heatmap and colorbar\\\", \\\"missingDataColor\\\": \\\"black\\\", \\\"referencePointLabel\\\": \\\"TSS\\\", \\\"yMin\\\": \\\"\\\", \\\"onePlotPerGroup\\\": \\\"False\\\", \\\"regionsLabel\\\": \\\"genes\\\", \\\"yMax\\\": \\\"\\\", \\\"endLabel\\\": \\\"TES\\\", \\\"sortRegions\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"startLabel\\\": \\\"TSS\\\", \\\"colorMap\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"heatmapHeight\\\": \\\"15.0\\\"}\", \"__rerun_remap_job_id__\": null, \"matrixFile\": \"null\"}", 
-            "tool_version": "1.0.3", 
-            "type": "tool", 
-            "user_outputs": []
-        }
-    }
-}
\ No newline at end of file
--- a/Galaxy-Workflow-Compute_and_correct_GC_bias.ga	Tue Feb 04 13:46:24 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,145 +0,0 @@
-{
-    "a_galaxy_workflow": "true", 
-    "annotation": "", 
-    "format-version": "0.1", 
-    "name": "Compute and correct GC bias", 
-    "steps": {
-        "0": {
-            "annotation": "must be a sorted BAM file", 
-            "id": 0, 
-            "input_connections": {}, 
-            "inputs": [
-                {
-                    "description": "must be a sorted BAM file", 
-                    "name": "BAM file to be checked for GC bias"
-                }
-            ], 
-            "name": "Input dataset", 
-            "outputs": [], 
-            "position": {
-                "left": 111, 
-                "top": 420
-            }, 
-            "tool_errors": null, 
-            "tool_id": null, 
-            "tool_state": "{\"name\": \"BAM file to be checked for GC bias\"}", 
-            "tool_version": null, 
-            "type": "data_input", 
-            "user_outputs": []
-        }, 
-        "1": {
-            "annotation": "**Computationall;y intensive**", 
-            "id": 1, 
-            "input_connections": {
-                "bamInput": {
-                    "id": 0, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool computeGCBias", 
-                    "name": "region"
-                }, 
-                {
-                    "description": "runtime parameter for tool computeGCBias", 
-                    "name": "source"
-                }, 
-                {
-                    "description": "runtime parameter for tool computeGCBias", 
-                    "name": "effectiveGenomeSize"
-                }, 
-                {
-                    "description": "runtime parameter for tool computeGCBias", 
-                    "name": "image_format"
-                }, 
-                {
-                    "description": "runtime parameter for tool computeGCBias", 
-                    "name": "fragmentLength"
-                }
-            ], 
-            "name": "computeGCBias", 
-            "outputs": [
-                {
-                    "name": "outFileName", 
-                    "type": "tabular"
-                }, 
-                {
-                    "name": "outImageName", 
-                    "type": "png"
-                }
-            ], 
-            "position": {
-                "left": 383.6166687011719, 
-                "top": 270.1166687011719
-            }, 
-            "post_job_actions": {
-                "HideDatasetActionoutFileName": {
-                    "action_arguments": {}, 
-                    "action_type": "HideDatasetAction", 
-                    "output_name": "outFileName"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeGCBias/1.0.3", 
-            "tool_state": "{\"__page__\": 0, \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bamInput\": \"null\", \"source\": \"{\\\"input1_2bit\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"ref_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"effectiveGenomeSize\": \"{\\\"effectiveGenomeSize_opt\\\": \\\"specific\\\", \\\"effectiveGenomeSize\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"advancedOpt\": \"{\\\"filterOut\\\": null, \\\"extraSampling\\\": null, \\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"sampleSize\\\": \\\"50000000\\\", \\\"__current_case__\\\": 1, \\\"regionSize\\\": \\\"300\\\"}\", \"image_format\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fragmentLength\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
-            "tool_version": "1.0.3", 
-            "type": "tool", 
-            "user_outputs": []
-        }, 
-        "2": {
-            "annotation": "", 
-            "id": 2, 
-            "input_connections": {
-                "GCbiasFrequenciesFile": {
-                    "id": 1, 
-                    "output_name": "outFileName"
-                }, 
-                "bamInput": {
-                    "id": 0, 
-                    "output_name": "output"
-                }
-            }, 
-            "inputs": [
-                {
-                    "description": "runtime parameter for tool correctGCBias", 
-                    "name": "region"
-                }, 
-                {
-                    "description": "runtime parameter for tool correctGCBias", 
-                    "name": "source"
-                }, 
-                {
-                    "description": "runtime parameter for tool correctGCBias", 
-                    "name": "effectiveGenomeSize"
-                }
-            ], 
-            "name": "correctGCBias", 
-            "outputs": [
-                {
-                    "name": "outFileName", 
-                    "type": "bam"
-                }
-            ], 
-            "position": {
-                "left": 779.61669921875, 
-                "top": 334.1166687011719
-            }, 
-            "post_job_actions": {
-                "RenameDatasetActionoutFileName": {
-                    "action_arguments": {
-                        "newname": "GCcorrected BAM file"
-                    }, 
-                    "action_type": "RenameDatasetAction", 
-                    "output_name": "outFileName"
-                }
-            }, 
-            "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_correctGCBias/1.0.3", 
-            "tool_state": "{\"__page__\": 0, \"region\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bamInput\": \"null\", \"source\": \"{\\\"input1_2bit\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"ref_source\\\": \\\"cached\\\", \\\"__current_case__\\\": 0}\", \"effectiveGenomeSize\": \"{\\\"effectiveGenomeSize_opt\\\": \\\"specific\\\", \\\"effectiveGenomeSize\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"GCbiasFrequenciesFile\": \"null\", \"advancedOpt\": \"{\\\"showAdvancedOpt\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"binSize\\\": \\\"50\\\"}\", \"__rerun_remap_job_id__\": null}", 
-            "tool_version": "1.0.3", 
-            "type": "tool", 
-            "user_outputs": []
-        }
-    }
-}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Remove_chr_from_the_beginning_of_genomic_interval_files.ga	Thu Apr 03 11:02:03 2014 -0400
@@ -0,0 +1,68 @@
+{
+    "a_galaxy_workflow": "true", 
+    "annotation": "", 
+    "format-version": "0.1", 
+    "name": "Remove 'chr' from the beginning of genomic interval files", 
+    "steps": {
+        "0": {
+            "annotation": "", 
+            "id": 0, 
+            "input_connections": {}, 
+            "inputs": [
+                {
+                    "description": "", 
+                    "name": "any column-based file of genomic intervals"
+                }
+            ], 
+            "name": "Input dataset", 
+            "outputs": [], 
+            "position": {
+                "left": 268.5, 
+                "top": 182.5
+            }, 
+            "tool_errors": null, 
+            "tool_id": null, 
+            "tool_state": "{\"name\": \"any column-based file of genomic intervals\"}", 
+            "tool_version": null, 
+            "type": "data_input", 
+            "user_outputs": []
+        }, 
+        "1": {
+            "annotation": "", 
+            "id": 1, 
+            "input_connections": {
+                "input1": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Trim", 
+            "outputs": [
+                {
+                    "name": "out_file1", 
+                    "type": "input"
+                }
+            ], 
+            "position": {
+                "left": 552, 
+                "top": 168
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionout_file1": {
+                    "action_arguments": {
+                        "newname": "removed \"chr\""
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "out_file1"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "trimmer", 
+            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"end\": \"\\\"0\\\"\", \"fastq\": \"\\\"\\\"\", \"ignore\": \"\\\"35\\\"\", \"start\": \"\\\"4\\\"\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/data2/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/mm9.len\\\"\", \"col\": \"\\\"1\\\"\"}", 
+            "tool_version": "0.0.1", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- a/repository_dependencies.xml	Tue Feb 04 13:46:24 2014 -0500
+++ b/repository_dependencies.xml	Thu Apr 03 11:02:03 2014 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
-<repositories description="These workflows require the deepTools repository.">
-    <repository changeset_revision="3fc7efe86cfc" name="deeptools" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+<repositories description="These workflows requires the deepTools repository.">
+    <repository changeset_revision="7d6d2f91843e" name="deeptools" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
 </repositories>