changeset 5:4bf23bc4f4e2 draft

Update workflows and dependencies
author stemcellcommons
date Fri, 22 Jul 2016 00:07:10 -0400
parents c9a9e3a09f44
children e6d80da34425
files TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga TF_ChIP-Seq_analysis_using_MACS2__hg19.ga TF_ChIP-Seq_analysis_using_MACS2__mm10.ga repository_dependencies.xml
diffstat 4 files changed, 445 insertions(+), 108 deletions(-) [+]
line wrap: on
line diff
--- a/TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga	Tue Jul 19 14:44:20 2016 -0400
+++ b/TF_ChIP-Seq_analysis_using_MACS2__danRer7.ga	Fri Jul 22 00:07:10 2016 -0400
@@ -27,7 +27,7 @@
             "tool_state": "{\"name\": \"exp_file\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "uuid": "dd984d64-daac-4547-9989-9303056523d3", 
+            "uuid": "e1db5f1d-b05b-4ecd-a194-0a1b37eec5c3", 
             "workflow_outputs": []
         }, 
         "1": {
@@ -53,7 +53,7 @@
             "tool_state": "{\"name\": \"input_file\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "uuid": "7a325193-5665-4aaf-9b87-c719769f9b71", 
+            "uuid": "369ab95a-3497-48c7-80c1-586ad71d8c14", 
             "workflow_outputs": []
         }, 
         "2": {
@@ -66,7 +66,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool FASTQ Parallel Groomer", 
+                    "name": "input_file"
+                }
+            ], 
             "label": null, 
             "name": "FASTQ Parallel Groomer", 
             "outputs": [
@@ -82,10 +87,16 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 
-            "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"options_type_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1, \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"null\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "66ca0d174cf2", 
+                "name": "fastq_groomer_parallel", 
+                "owner": "kevyin", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"__current_case__\\\": 1, \\\"options_type_selector\\\": \\\"advanced\\\", \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
             "tool_version": "0.3.1", 
             "type": "tool", 
-            "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", 
+            "uuid": "b81ef5b7-b1dc-440d-a441-8ecd1953626d", 
             "workflow_outputs": []
         }, 
         "3": {
@@ -98,7 +109,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool FASTQ Parallel Groomer", 
+                    "name": "input_file"
+                }
+            ], 
             "label": null, 
             "name": "FASTQ Parallel Groomer", 
             "outputs": [
@@ -114,10 +130,16 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 
-            "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"options_type_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1, \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"null\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "66ca0d174cf2", 
+                "name": "fastq_groomer_parallel", 
+                "owner": "kevyin", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"__current_case__\\\": 1, \\\"options_type_selector\\\": \\\"advanced\\\", \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
             "tool_version": "0.3.1", 
             "type": "tool", 
-            "uuid": "259e1093-ff1c-4f65-8432-97d5124af250", 
+            "uuid": "9e279dc6-3a13-47e6-8252-148f3473a0fb", 
             "workflow_outputs": []
         }, 
         "4": {
@@ -130,7 +152,12 @@
                     "output_name": "output_file"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Map with Bowtie for Illumina", 
+                    "name": "singlePaired"
+                }
+            ], 
             "label": null, 
             "name": "Map with Bowtie for Illumina", 
             "outputs": [
@@ -162,10 +189,16 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", 
-            "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"danRer7\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"False\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"False\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "df86f29bedee", 
+                "name": "bowtie_wrappers", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"danRer7\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"false\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"false\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", 
             "tool_version": "1.1.3", 
             "type": "tool", 
-            "uuid": "cd8dda4a-0a66-415c-98f0-0d6361a1abb0", 
+            "uuid": "2e9e48d6-45dd-47fb-9b8d-de51fd2f35c0", 
             "workflow_outputs": []
         }, 
         "5": {
@@ -178,7 +211,12 @@
                     "output_name": "output_file"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Map with Bowtie for Illumina", 
+                    "name": "singlePaired"
+                }
+            ], 
             "label": null, 
             "name": "Map with Bowtie for Illumina", 
             "outputs": [
@@ -210,15 +248,21 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", 
-            "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"danRer7\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"False\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"False\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "df86f29bedee", 
+                "name": "bowtie_wrappers", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"danRer7\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"false\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"false\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", 
             "tool_version": "1.1.3", 
             "type": "tool", 
-            "uuid": "a09286be-e5ba-45fb-be1f-585fe79cf677", 
+            "uuid": "9b5ea3b7-4c70-4dd1-91ac-0201897bfe74", 
             "workflow_outputs": []
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         "6": {
             "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", 
             "id": 6, 
             "input_connections": {
                 "source|input1": {
@@ -226,7 +270,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool SAM-to-BAM", 
+                    "name": "source"
+                }
+            ], 
             "label": null, 
             "name": "SAM-to-BAM", 
             "outputs": [
@@ -241,16 +290,22 @@
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", 
-            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"danRer7full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
-            "tool_version": "2.1", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "d04d9f1c6791", 
+                "name": "sam_to_bam", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"danRer7\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
+            "tool_version": "2.0", 
             "type": "tool", 
-            "uuid": "03872d2a-dde5-4152-a256-04cddf41fec0", 
+            "uuid": "2e04c1f9-8079-4561-892d-c3e2c30e4702", 
             "workflow_outputs": []
         }, 
         "7": {
             "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", 
             "id": 7, 
             "input_connections": {
                 "source|input1": {
@@ -258,7 +313,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool SAM-to-BAM", 
+                    "name": "source"
+                }
+            ], 
             "label": null, 
             "name": "SAM-to-BAM", 
             "outputs": [
@@ -273,11 +333,17 @@
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", 
-            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"danRer7full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
-            "tool_version": "2.1", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "d04d9f1c6791", 
+                "name": "sam_to_bam", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"danRer7\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
+            "tool_version": "2.0", 
             "type": "tool", 
-            "uuid": "1a747633-c084-433c-8ca5-1f1196e3791f", 
+            "uuid": "11a847f3-7d2e-44b2-9cd6-ee9285508002", 
             "workflow_outputs": []
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         "8": {
@@ -294,7 +360,16 @@
                     "output_name": "output1"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool MACS2 callpeak", 
+                    "name": "input_control_file"
+                }, 
+                {
+                    "description": "runtime parameter for tool MACS2 callpeak", 
+                    "name": "input_treatment_file"
+                }
+            ], 
             "label": null, 
             "name": "MACS2 callpeak", 
             "outputs": [
@@ -342,10 +417,16 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", 
-            "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"gsize\\\": \\\"1400000000\\\", \\\"effective_genome_size_options_selector\\\": \\\"user_defined\\\", \\\"__current_case__\\\": 4}\", \"bampe\": \"\\\"False\\\"\", \"input_control_file\": \"null\", \"__rerun_remap_job_id__\": null, \"outputs\": \"[\\\"peaks_tabular\\\", \\\"bdg\\\", \\\"pdf\\\"]\", \"cutoff_options\": \"{\\\"cutoff_options_selector\\\": \\\"qvalue\\\", \\\"qvalue\\\": \\\"0.05\\\", \\\"__current_case__\\\": 1}\", \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"off\\\", \\\"__current_case__\\\": 1}\", \"input_treatment_file\": \"null\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 0}\", \"band_width\": \"\\\"300\\\"\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "6d4babad010f", 
+                "name": "macs2", 
+                "owner": "iuc", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"gsize\\\": \\\"1400000000\\\", \\\"effective_genome_size_options_selector\\\": \\\"user_defined\\\", \\\"__current_case__\\\": 4}\", \"bampe\": \"\\\"false\\\"\", \"input_control_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"outputs\": \"[\\\"peaks_tabular\\\", \\\"bdg\\\", \\\"pdf\\\"]\", \"cutoff_options\": \"{\\\"cutoff_options_selector\\\": \\\"qvalue\\\", \\\"qvalue\\\": \\\"0.05\\\", \\\"__current_case__\\\": 1}\", \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"off\\\", \\\"__current_case__\\\": 1}\", \"input_treatment_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 0}\", \"band_width\": \"\\\"300\\\"\"}", 
             "tool_version": "2.1.0.20151222.0", 
             "type": "tool", 
-            "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7", 
+            "uuid": "ee77dbd1-6b19-4faa-bcb5-b71db4348aaa", 
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         }, 
         "9": {
@@ -362,7 +443,16 @@
                     "output_name": "output_treat_pileup"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool MACS2 bdgcmp", 
+                    "name": "infile_control"
+                }, 
+                {
+                    "description": "runtime parameter for tool MACS2 bdgcmp", 
+                    "name": "infile_treatment"
+                }
+            ], 
             "label": null, 
             "name": "MACS2 bdgcmp", 
             "outputs": [
@@ -378,10 +468,16 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", 
-            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"null\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"null\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "6d4babad010f", 
+                "name": "macs2", 
+                "owner": "iuc", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
             "tool_version": "2.1.0.20151222.0", 
             "type": "tool", 
-            "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", 
+            "uuid": "17a78c22-1f86-42bc-93e3-f0d05f8b8cb2", 
             "workflow_outputs": []
         }, 
         "10": {
@@ -394,7 +490,12 @@
                     "output_name": "outfile"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Wig/BedGraph-to-bigWig", 
+                    "name": "input1"
+                }
+            ], 
             "label": null, 
             "name": "Wig/BedGraph-to-bigWig", 
             "outputs": [
@@ -410,12 +511,12 @@
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             "tool_id": "wig_to_bigWig", 
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+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", 
             "tool_version": "1.1.0", 
             "type": "tool", 
-            "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", 
+            "uuid": "909d96be-b7be-487e-b9e5-5e5b8e5126bd", 
             "workflow_outputs": []
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     }, 
-    "uuid": "1008a9d1-09b6-465e-9515-6cad350b4089"
+    "uuid": "6a85dafd-cfde-4b35-988e-1bc4c0c93b94"
 }
\ No newline at end of file
--- a/TF_ChIP-Seq_analysis_using_MACS2__hg19.ga	Tue Jul 19 14:44:20 2016 -0400
+++ b/TF_ChIP-Seq_analysis_using_MACS2__hg19.ga	Fri Jul 22 00:07:10 2016 -0400
@@ -6,6 +6,7 @@
     "steps": {
         "0": {
             "annotation": "", 
+            "content_id": null, 
             "id": 0, 
             "input_connections": {}, 
             "inputs": [
@@ -14,6 +15,7 @@
                     "name": "exp_file"
                 }
             ], 
+            "label": null, 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
@@ -25,10 +27,12 @@
             "tool_state": "{\"name\": \"exp_file\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "user_outputs": []
+            "uuid": "f48e77b8-7d87-4b9f-bac1-6bd9748addab", 
+            "workflow_outputs": []
         }, 
         "1": {
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+            "content_id": null, 
             "id": 1, 
             "input_connections": {}, 
             "inputs": [
@@ -37,6 +41,7 @@
                     "name": "input_file"
                 }
             ], 
+            "label": null, 
             "name": "Input dataset", 
             "outputs": [], 
             "position": {
@@ -48,10 +53,12 @@
             "tool_state": "{\"name\": \"input_file\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "user_outputs": []
+            "uuid": "d38090b9-b25b-4fea-948e-f5818b1d2d4f", 
+            "workflow_outputs": []
         }, 
         "2": {
             "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 
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             "input_connections": {
                 "input_file": {
@@ -59,7 +66,13 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool FASTQ Parallel Groomer", 
+                    "name": "input_file"
+                }
+            ], 
+            "label": null, 
             "name": "FASTQ Parallel Groomer", 
             "outputs": [
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@@ -74,13 +87,21 @@
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             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 
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+            "tool_shed_repository": {
+                "changeset_revision": "66ca0d174cf2", 
+                "name": "fastq_groomer_parallel", 
+                "owner": "kevyin", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"__current_case__\\\": 1, \\\"options_type_selector\\\": \\\"advanced\\\", \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
             "tool_version": "0.3.1", 
             "type": "tool", 
-            "user_outputs": []
+            "uuid": "c2e08189-33e3-40bf-a914-cfdb726734e5", 
+            "workflow_outputs": []
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         "3": {
             "annotation": "", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 
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             "input_connections": {
                 "input_file": {
@@ -88,7 +109,13 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool FASTQ Parallel Groomer", 
+                    "name": "input_file"
+                }
+            ], 
+            "label": null, 
             "name": "FASTQ Parallel Groomer", 
             "outputs": [
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@@ -103,13 +130,21 @@
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             "type": "tool", 
-            "user_outputs": []
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+            "workflow_outputs": []
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@@ -117,7 +152,13 @@
                     "output_name": "output_file"
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             "name": "Map with Bowtie for Illumina", 
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@@ -148,13 +189,21 @@
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@@ -162,7 +211,13 @@
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             "name": "Map with Bowtie for Illumina", 
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@@ -207,7 +270,13 @@
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@@ -221,14 +290,22 @@
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+                "owner": "devteam", 
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@@ -236,7 +313,13 @@
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@@ -250,14 +333,22 @@
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@@ -269,7 +360,17 @@
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@@ -334,7 +443,17 @@
                     "output_name": "output_treat_pileup"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool MACS2 bdgcmp", 
+                    "name": "infile_control"
+                }, 
+                {
+                    "description": "runtime parameter for tool MACS2 bdgcmp", 
+                    "name": "infile_treatment"
+                }
+            ], 
+            "label": null, 
             "name": "MACS2 bdgcmp", 
             "outputs": [
                 {
@@ -349,13 +468,21 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", 
-            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"null\", \"infile_treatment\": \"null\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "6d4babad010f", 
+                "name": "macs2", 
+                "owner": "iuc", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
             "tool_version": "2.1.0.20151222.0", 
             "type": "tool", 
-            "user_outputs": []
+            "uuid": "dcfd9cac-e8a2-4425-a8fc-1e398710d6ca", 
+            "workflow_outputs": []
         }, 
         "10": {
             "annotation": "{\"out_file1\": {\"name\": \"MACS2_bigwig\", \"description\": \"\", \"type\": \"bigwig\"}}", 
+            "content_id": "wig_to_bigWig", 
             "id": 10, 
             "input_connections": {
                 "input1": {
@@ -363,7 +490,13 @@
                     "output_name": "outfile"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Wig/BedGraph-to-bigWig", 
+                    "name": "input1"
+                }
+            ], 
+            "label": null, 
             "name": "Wig/BedGraph-to-bigWig", 
             "outputs": [
                 {
@@ -378,10 +511,12 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "wig_to_bigWig", 
-            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", 
             "tool_version": "1.1.0", 
             "type": "tool", 
-            "user_outputs": []
+            "uuid": "f5cf8c55-03d2-4fc0-b5fa-5f4be859b628", 
+            "workflow_outputs": []
         }
-    }
+    }, 
+    "uuid": "9d3dbd7d-2fd7-479f-a582-aa2d84a5d443"
 }
\ No newline at end of file
--- a/TF_ChIP-Seq_analysis_using_MACS2__mm10.ga	Tue Jul 19 14:44:20 2016 -0400
+++ b/TF_ChIP-Seq_analysis_using_MACS2__mm10.ga	Fri Jul 22 00:07:10 2016 -0400
@@ -27,7 +27,7 @@
             "tool_state": "{\"name\": \"exp_file\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "uuid": "dd984d64-daac-4547-9989-9303056523d3", 
+            "uuid": "77699462-04dc-4480-a351-c3ba909c94d9", 
             "workflow_outputs": []
         }, 
         "1": {
@@ -53,7 +53,7 @@
             "tool_state": "{\"name\": \"input_file\"}", 
             "tool_version": null, 
             "type": "data_input", 
-            "uuid": "7a325193-5665-4aaf-9b87-c719769f9b71", 
+            "uuid": "87084ec7-ede5-4f5a-a49c-5f96c169daa7", 
             "workflow_outputs": []
         }, 
         "2": {
@@ -66,7 +66,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool FASTQ Parallel Groomer", 
+                    "name": "input_file"
+                }
+            ], 
             "label": null, 
             "name": "FASTQ Parallel Groomer", 
             "outputs": [
@@ -82,10 +87,16 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 
-            "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"options_type_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1, \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"null\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "66ca0d174cf2", 
+                "name": "fastq_groomer_parallel", 
+                "owner": "kevyin", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"__current_case__\\\": 1, \\\"options_type_selector\\\": \\\"advanced\\\", \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
             "tool_version": "0.3.1", 
             "type": "tool", 
-            "uuid": "83fb115f-30f9-4971-a6dc-416bc1206f1f", 
+            "uuid": "a91fcfa1-2ad2-4d1b-af4e-8c348ca99cf4", 
             "workflow_outputs": []
         }, 
         "3": {
@@ -98,7 +109,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool FASTQ Parallel Groomer", 
+                    "name": "input_file"
+                }
+            ], 
             "label": null, 
             "name": "FASTQ Parallel Groomer", 
             "outputs": [
@@ -114,10 +130,16 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/kevyin/fastq_groomer_parallel/fastq_groomer_parallel/0.3.1", 
-            "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"options_type_selector\\\": \\\"advanced\\\", \\\"__current_case__\\\": 1, \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"null\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "66ca0d174cf2", 
+                "name": "fastq_groomer_parallel", 
+                "owner": "kevyin", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"input_type\": \"\\\"sanger\\\"\", \"__rerun_remap_job_id__\": null, \"options_type\": \"{\\\"output_type\\\": \\\"sanger\\\", \\\"force_quality_encoding\\\": \\\"ascii\\\", \\\"__current_case__\\\": 1, \\\"options_type_selector\\\": \\\"advanced\\\", \\\"summarize_input\\\": \\\"dont_summarize_input\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
             "tool_version": "0.3.1", 
             "type": "tool", 
-            "uuid": "259e1093-ff1c-4f65-8432-97d5124af250", 
+            "uuid": "93829f40-3abf-4aa3-8951-46b67cf86a95", 
             "workflow_outputs": []
         }, 
         "4": {
@@ -130,7 +152,12 @@
                     "output_name": "output_file"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Map with Bowtie for Illumina", 
+                    "name": "singlePaired"
+                }
+            ], 
             "label": null, 
             "name": "Map with Bowtie for Illumina", 
             "outputs": [
@@ -162,10 +189,16 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", 
-            "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm10\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"False\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"False\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "df86f29bedee", 
+                "name": "bowtie_wrappers", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm10\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"false\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"false\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", 
             "tool_version": "1.1.3", 
             "type": "tool", 
-            "uuid": "cd8dda4a-0a66-415c-98f0-0d6361a1abb0", 
+            "uuid": "9ec994d9-7309-4655-b3d8-cca2de8de69b", 
             "workflow_outputs": []
         }, 
         "5": {
@@ -178,7 +211,12 @@
                     "output_name": "output_file"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Map with Bowtie for Illumina", 
+                    "name": "singlePaired"
+                }
+            ], 
             "label": null, 
             "name": "Map with Bowtie for Illumina", 
             "outputs": [
@@ -210,15 +248,21 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie_wrappers/bowtie_wrapper/1.1.3", 
-            "tool_state": "{\"suppressHeader\": \"\\\"False\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm10\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": null, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"False\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"False\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "df86f29bedee", 
+                "name": "bowtie_wrappers", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"suppressHeader\": \"\\\"false\\\"\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"mm10\\\", \\\"__current_case__\\\": 0}\", \"singlePaired\": \"{\\\"sInput1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"sParams\\\": {\\\"sForwardAlign\\\": \\\"forward\\\", \\\"sTrimH\\\": \\\"0\\\", \\\"sTrimL\\\": \\\"0\\\", \\\"sUnmappedFile\\\": \\\"false\\\", \\\"sSettingsType\\\": \\\"full\\\", \\\"sSuppressAlign\\\": \\\"1\\\", \\\"sAlignLimit\\\": \\\"-1\\\", \\\"sMaxFile\\\": \\\"false\\\", \\\"sReverseAlign\\\": \\\"reverse\\\", \\\"__current_case__\\\": 1, \\\"sSkip\\\": \\\"0\\\", \\\"sBestOption\\\": {\\\"sTryHardOption\\\": {\\\"sTryHard\\\": \\\"noTryHard\\\", \\\"__current_case__\\\": 0, \\\"snMaxBacktracks\\\": \\\"125\\\"}, \\\"sBest\\\": \\\"noBest\\\", \\\"__current_case__\\\": 0}, \\\"alignModeOption\\\": {\\\"sMismatchSeed\\\": \\\"2\\\", \\\"sMismatchQual\\\": \\\"70\\\", \\\"sRounding\\\": \\\"round\\\", \\\"__current_case__\\\": 0, \\\"alignMode\\\": \\\"nMode\\\", \\\"sSeedLen\\\": \\\"28\\\"}, \\\"sOffrate\\\": \\\"-1\\\", \\\"sSeed\\\": \\\"0\\\", \\\"sAllValAlignsOption\\\": {\\\"sAllValAligns\\\": \\\"noAllValAligns\\\", \\\"sValAlign\\\": \\\"1\\\", \\\"__current_case__\\\": 0}}, \\\"sPaired\\\": \\\"single\\\", \\\"__current_case__\\\": 0}\"}", 
             "tool_version": "1.1.3", 
             "type": "tool", 
-            "uuid": "a09286be-e5ba-45fb-be1f-585fe79cf677", 
+            "uuid": "20e8c743-50c8-4afa-9fda-54b0207d7e8f", 
             "workflow_outputs": []
         }, 
         "6": {
             "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", 
             "id": 6, 
             "input_connections": {
                 "source|input1": {
@@ -226,7 +270,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool SAM-to-BAM", 
+                    "name": "source"
+                }
+            ], 
             "label": null, 
             "name": "SAM-to-BAM", 
             "outputs": [
@@ -241,16 +290,22 @@
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", 
-            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm10full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
-            "tool_version": "2.1", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "d04d9f1c6791", 
+                "name": "sam_to_bam", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm10\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
+            "tool_version": "2.0", 
             "type": "tool", 
-            "uuid": "03872d2a-dde5-4152-a256-04cddf41fec0", 
+            "uuid": "5c875347-40cd-4522-a57a-ca380f976df4", 
             "workflow_outputs": []
         }, 
         "7": {
             "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", 
             "id": 7, 
             "input_connections": {
                 "source|input1": {
@@ -258,7 +313,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool SAM-to-BAM", 
+                    "name": "source"
+                }
+            ], 
             "label": null, 
             "name": "SAM-to-BAM", 
             "outputs": [
@@ -273,11 +333,17 @@
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1", 
-            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm10full\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
-            "tool_version": "2.1", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "d04d9f1c6791", 
+                "name": "sam_to_bam", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"source\": \"{\\\"index_source\\\": \\\"cached\\\", \\\"index\\\": \\\"mm10\\\", \\\"input1\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
+            "tool_version": "2.0", 
             "type": "tool", 
-            "uuid": "1a747633-c084-433c-8ca5-1f1196e3791f", 
+            "uuid": "6f3e360c-d5b4-46bb-9a3d-e56c78651cee", 
             "workflow_outputs": []
         }, 
         "8": {
@@ -294,7 +360,16 @@
                     "output_name": "output1"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool MACS2 callpeak", 
+                    "name": "input_control_file"
+                }, 
+                {
+                    "description": "runtime parameter for tool MACS2 callpeak", 
+                    "name": "input_treatment_file"
+                }
+            ], 
             "label": null, 
             "name": "MACS2 callpeak", 
             "outputs": [
@@ -342,10 +417,16 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.0.20151222.0", 
-            "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2150570000\\\", \\\"__current_case__\\\": 1}\", \"bampe\": \"\\\"False\\\"\", \"input_control_file\": \"null\", \"__rerun_remap_job_id__\": null, \"outputs\": \"[\\\"peaks_tabular\\\", \\\"bdg\\\", \\\"pdf\\\"]\", \"cutoff_options\": \"{\\\"cutoff_options_selector\\\": \\\"qvalue\\\", \\\"qvalue\\\": \\\"0.05\\\", \\\"__current_case__\\\": 1}\", \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"off\\\", \\\"__current_case__\\\": 1}\", \"input_treatment_file\": \"null\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 0}\", \"band_width\": \"\\\"300\\\"\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "6d4babad010f", 
+                "name": "macs2", 
+                "owner": "iuc", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"effective_genome_size_options\": \"{\\\"effective_genome_size_options_selector\\\": \\\"2150570000\\\", \\\"__current_case__\\\": 1}\", \"bampe\": \"\\\"false\\\"\", \"input_control_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"outputs\": \"[\\\"peaks_tabular\\\", \\\"bdg\\\", \\\"pdf\\\"]\", \"cutoff_options\": \"{\\\"cutoff_options_selector\\\": \\\"qvalue\\\", \\\"qvalue\\\": \\\"0.05\\\", \\\"__current_case__\\\": 1}\", \"advanced_options\": \"{\\\"advanced_options_selector\\\": \\\"off\\\", \\\"__current_case__\\\": 1}\", \"input_treatment_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"nomodel_type\": \"{\\\"nomodel_type_selector\\\": \\\"create_model\\\", \\\"__current_case__\\\": 0}\", \"band_width\": \"\\\"300\\\"\"}", 
             "tool_version": "2.1.0.20151222.0", 
             "type": "tool", 
-            "uuid": "e8e38d74-1a63-4c58-b042-487838e9edc7", 
+            "uuid": "bbcb3034-f9af-4b45-b877-54822312ddac", 
             "workflow_outputs": []
         }, 
         "9": {
@@ -362,7 +443,16 @@
                     "output_name": "output_treat_pileup"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool MACS2 bdgcmp", 
+                    "name": "infile_control"
+                }, 
+                {
+                    "description": "runtime parameter for tool MACS2 bdgcmp", 
+                    "name": "infile_treatment"
+                }
+            ], 
             "label": null, 
             "name": "MACS2 bdgcmp", 
             "outputs": [
@@ -378,10 +468,16 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_bdgcmp/2.1.0.20151222.0", 
-            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"null\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"null\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "6d4babad010f", 
+                "name": "macs2", 
+                "owner": "iuc", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"infile_control\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"bdgcmp_options\": \"{\\\"bdgcmp_options_selector\\\": \\\"ppois\\\", \\\"__current_case__\\\": 3}\", \"infile_treatment\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
             "tool_version": "2.1.0.20151222.0", 
             "type": "tool", 
-            "uuid": "974626f2-7adb-4f71-9db5-7abdff78e5d0", 
+            "uuid": "21c64164-b151-4bc4-88c8-3c3a68401a41", 
             "workflow_outputs": []
         }, 
         "10": {
@@ -394,7 +490,12 @@
                     "output_name": "outfile"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Wig/BedGraph-to-bigWig", 
+                    "name": "input1"
+                }
+            ], 
             "label": null, 
             "name": "Wig/BedGraph-to-bigWig", 
             "outputs": [
@@ -410,12 +511,12 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "wig_to_bigWig", 
-            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"settings\": \"{\\\"settingsType\\\": \\\"preset\\\", \\\"__current_case__\\\": 0}\"}", 
             "tool_version": "1.1.0", 
             "type": "tool", 
-            "uuid": "c9d04953-8508-4b6b-bbf3-edcf421eadc8", 
+            "uuid": "de37a72c-ebc2-4f4f-9e80-70b11d1be79a", 
             "workflow_outputs": []
         }
     }, 
-    "uuid": "a2493925-4c14-413d-89d6-0b3ba2395dbe"
+    "uuid": "3be7b1f8-3931-40c8-8bb1-7fffbe2826d4"
 }
\ No newline at end of file
--- a/repository_dependencies.xml	Tue Jul 19 14:44:20 2016 -0400
+++ b/repository_dependencies.xml	Fri Jul 22 00:07:10 2016 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<repositories description="Stem Cell Commons TF ChIP-seq workflow for hg19">
+<repositories description="Stem Cell Commons TF ChIP-seq workflows">
   <repository toolshed="toolshed.g2.bx.psu.edu" name="fastq_groomer_parallel" owner="kevyin" changeset_revision="66ca0d174cf2" />
   <repository toolshed="toolshed.g2.bx.psu.edu" name="bowtie_wrappers" owner="devteam" changeset_revision="df86f29bedee" />
-  <repository toolshed="toolshed.g2.bx.psu.edu" name="sam_to_bam" owner="devteam" changeset_revision="881e16ad05c6" />
+  <repository toolshed="toolshed.g2.bx.psu.edu" name="sam_to_bam" owner="devteam" changeset_revision="d04d9f1c6791" />
   <repository toolshed="toolshed.g2.bx.psu.edu" name="macs2" owner="iuc" changeset_revision="6d4babad010f" />
 </repositories>