--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-1.ga	Mon Apr 11 13:14:14 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-1.ga	Fri May 13 05:46:40 2016 -0400
@@ -19,7 +19,7 @@
             "name": "Input dataset collection", 
             "outputs": [], 
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+                "left": 192.9375, 
                 "top": 200
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@@ -106,6 +106,12 @@
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             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.4", 
+            "tool_shed_repository": {
+                "changeset_revision": "befdb392fece", 
+                "name": "fetch_fasta_from_ncbi", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"queryString\": \"\\\"${ncbi_guide_ID}\\\"\", \"dbname\": \"\\\"nuccore\\\"\"}", 
             "tool_version": "0.9.4", 
             "type": "tool", 
@@ -128,7 +134,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Clip adapter", 
+                    "name": "input"
+                }
+            ], 
             "label": null, 
             "name": "Clip adapter", 
             "outputs": [
@@ -144,7 +155,13 @@
             "post_job_actions": {}, 
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             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", 
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+            "tool_shed_repository": {
+                "changeset_revision": "91cce7c1436d", 
+                "name": "yac_clipper", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"out_format\": \"\\\"fasta\\\"\", \"__page__\": 0, \"min\": \"\\\"18\\\"\", \"max\": \"\\\"30\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"459d9188801e11e5ae6af01fafdfc061\\\"\", \"clip_source\": \"{\\\"clip_source_list\\\": \\\"prebuilt\\\", \\\"clip_sequence\\\": \\\"CTGTAGGCACCATCAATCGT\\\", \\\"__current_case__\\\": 0}\", \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"Nmode\": \"\\\"reject\\\"\"}", 
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@@ -166,7 +183,16 @@
                     "output_name": "outfilename"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool NCBI BLAST+ makeblastdb", 
+                    "name": "mask_data_file"
+                }, 
+                {
+                    "description": "runtime parameter for tool NCBI BLAST+ makeblastdb", 
+                    "name": "input_file"
+                }
+            ], 
             "label": null, 
             "name": "NCBI BLAST+ makeblastdb", 
             "outputs": [
@@ -188,7 +214,13 @@
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             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", 
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+            "tool_shed_repository": {
+                "changeset_revision": "577d9c12411a", 
+                "name": "ncbi_blast_plus", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"input_file\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"true\\\"\", \"tax\": \"{\\\"__current_case__\\\": 0, \\\"taxselect\\\": \\\"\\\"}\", \"__workflow_invocation_uuid__\": \"\\\"ae5b2b58802911e5808df01fafdfc061\\\"\", \"title\": \"\\\"Blastn candidate database\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"parse_seqids\": \"\\\"false\\\"\"}", 
             "tool_version": "0.1.06", 
             "type": "tool", 
             "uuid": "ce29cdbe-653a-4d0e-b225-0d0762c28d4d", 
@@ -204,7 +236,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Concatenate multiple datasets", 
+                    "name": "input"
+                }
+            ], 
             "label": null, 
             "name": "Concatenate multiple datasets", 
             "outputs": [
@@ -233,7 +270,13 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", 
-            "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
+            "tool_shed_repository": {
+                "changeset_revision": "201c568972c3", 
+                "name": "concatenate_multiple_datasets", 
+                "owner": "mvdbeek", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
             "tool_version": "0.2", 
             "type": "tool", 
             "uuid": "6be696ec-ca89-4e64-ad39-7d0e7fb4401a", 
@@ -249,7 +292,12 @@
                     "output_name": "out_file1"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool fasta - tabular", 
+                    "name": "switch"
+                }
+            ], 
             "label": null, 
             "name": "fasta - tabular", 
             "outputs": [
@@ -271,7 +319,13 @@
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             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", 
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+            "tool_shed_repository": {
+                "changeset_revision": "330dd8a8c31a", 
+                "name": "msp_fasta_tabular_converter", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 0, \\\"conversionType\\\": \\\"fasta2tabular\\\"}\", \"__rerun_remap_job_id__\": null}", 
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             "type": "tool", 
             "uuid": "32ec6fba-fb02-4edd-a3c3-3bd617e78ff2", 
@@ -287,7 +341,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool fasta - tabular", 
+                    "name": "switch"
+                }
+            ], 
             "label": null, 
             "name": "fasta - tabular", 
             "outputs": [
@@ -311,7 +370,13 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", 
-            "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"conversionType\\\": \\\"tabular2fastaweight\\\", \\\"__current_case__\\\": 2}\", \"__rerun_remap_job_id__\": null}", 
+            "tool_shed_repository": {
+                "changeset_revision": "330dd8a8c31a", 
+                "name": "msp_fasta_tabular_converter", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 2, \\\"conversionType\\\": \\\"tabular2fastaweight\\\"}\", \"__rerun_remap_job_id__\": null}", 
             "tool_version": "1.1.0", 
             "type": "tool", 
             "uuid": "7cc53603-6876-4f15-919d-177218404620", 
@@ -333,7 +398,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool sRbowtie", 
+                    "name": "input"
+                }
+            ], 
             "label": null, 
             "name": "sRbowtie", 
             "outputs": [
@@ -375,7 +445,13 @@
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             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", 
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+            "tool_shed_repository": {
+                "changeset_revision": "c1bfa227bbb6", 
+                "name": "msp_sr_bowtie", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"output_format\": \"\\\"tabular\\\"\", \"additional_fasta\": \"\\\"unal\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"dm6\\\", \\\"__current_case__\\\": 0}\", \"method\": \"\\\"k_option\\\"\"}", 
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             "type": "tool", 
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@@ -389,7 +465,7 @@
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+            "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.5", 
             "id": 9, 
             "input_connections": {
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@@ -420,9 +496,15 @@
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-            "tool_version": "1.1.4", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.5", 
+            "tool_shed_repository": {
+                "changeset_revision": "dc684e37f668", 
+                "name": "msp_oases", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
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+            "tool_state": "{\"__page__\": 0, \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}]\", \"end_hash_length\": \"\\\"29\\\"\", \"__rerun_remap_job_id__\": null, \"start_hash_length\": \"\\\"13\\\"\"}", 
+            "tool_version": "1.1.5", 
             "type": "tool", 
             "uuid": "4290f9b9-2ea7-4634-a639-bc008f1eb90c", 
             "workflow_outputs": [
@@ -447,7 +529,16 @@
                     "output_name": "transcripts"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool NCBI BLAST+ blastn", 
+                    "name": "db_opts"
+                }, 
+                {
+                    "description": "runtime parameter for tool NCBI BLAST+ blastn", 
+                    "name": "query"
+                }
+            ], 
             "label": null, 
             "name": "NCBI BLAST+ blastn", 
             "outputs": [
@@ -469,7 +560,13 @@
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+            "tool_shed_repository": {
+                "changeset_revision": "577d9c12411a", 
+                "name": "ncbi_blast_plus", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
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             "tool_version": "0.1.06", 
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@@ -489,7 +586,16 @@
                     "output_name": "transcripts"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Parse blast output and compile hits", 
+                    "name": "blast"
+                }, 
+                {
+                    "description": "runtime parameter for tool Parse blast output and compile hits", 
+                    "name": "sequences"
+                }
+            ], 
             "label": null, 
             "name": "Parse blast output and compile hits", 
             "outputs": [
@@ -528,7 +634,13 @@
             }, 
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+            "tool_shed_repository": {
+                "changeset_revision": "6dfa79a6908a", 
+                "name": "msp_blastparser_and_hits", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
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+            "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"filter_term_out\\\": \\\"JX220408.1\\\", \\\"filter_relativeCov\\\": \\\"0.0\\\", \\\"filter_meanScore\\\": \\\"0.0\\\", \\\"use_filters\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"filter_term_in\\\": \\\"Nora_virus\\\", \\\"filter_maxScore\\\": \\\"0.0\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"short\\\"\", \"sequences\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"blast\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
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@@ -555,7 +667,12 @@
                     "output_name": "fastaOutput"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool cap3", 
+                    "name": "inputSequences"
+                }
+            ], 
             "label": null, 
             "name": "cap3", 
             "outputs": [
@@ -635,7 +752,13 @@
             }, 
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             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_cap3/cap3/1.2.0", 
-            "tool_state": "{\"__page__\": 0, \"inputSequences\": \"null\", \"overlaplength\": \"\\\"40\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"ae5b2b58802911e5808df01fafdfc061\\\"\", \"overlapidentity\": \"\\\"90\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "ddb463fdf57e", 
+                "name": "msp_cap3", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"inputSequences\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"overlaplength\": \"\\\"40\\\"\", \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"ae5b2b58802911e5808df01fafdfc061\\\"\", \"overlapidentity\": \"\\\"90\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
             "tool_version": "1.2.0", 
             "type": "tool", 
             "uuid": "1d6dcdba-8f89-453b-ae30-6bb8aee06360", 
@@ -661,7 +784,16 @@
                     "output_name": "contigsandsinglets"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool NCBI BLAST+ blastn", 
+                    "name": "db_opts"
+                }, 
+                {
+                    "description": "runtime parameter for tool NCBI BLAST+ blastn", 
+                    "name": "query"
+                }
+            ], 
             "label": null, 
             "name": "NCBI BLAST+ blastn", 
             "outputs": [
@@ -683,7 +815,13 @@
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             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", 
-            "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"slen\\\"]}\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"ae5b2b58802911e5808df01fafdfc061\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastn\\\"\", \"query\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "577d9c12411a", 
+                "name": "ncbi_blast_plus", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"output\": \"{\\\"out_format\\\": \\\"cols\\\", \\\"std_cols\\\": [\\\"qseqid\\\", \\\"sseqid\\\", \\\"pident\\\", \\\"length\\\", \\\"mismatch\\\", \\\"gapopen\\\", \\\"qstart\\\", \\\"qend\\\", \\\"sstart\\\", \\\"send\\\", \\\"evalue\\\", \\\"bitscore\\\"], \\\"ids_cols\\\": null, \\\"tax_cols\\\": null, \\\"__current_case__\\\": 2, \\\"misc_cols\\\": null, \\\"ext_cols\\\": [\\\"slen\\\"]}\", \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"ae5b2b58802911e5808df01fafdfc061\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastn\\\"\", \"query\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
             "tool_version": "0.1.06", 
             "type": "tool", 
             "uuid": "c9f9c58a-f21d-46d2-a952-9e7b7d5bf939", 
@@ -707,7 +845,20 @@
                     "output_name": "contigsandsinglets"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool blast_to_scaffold", 
+                    "name": "guideSequence"
+                }, 
+                {
+                    "description": "runtime parameter for tool blast_to_scaffold", 
+                    "name": "blast_tab"
+                }, 
+                {
+                    "description": "runtime parameter for tool blast_to_scaffold", 
+                    "name": "sequences"
+                }
+            ], 
             "label": null, 
             "name": "blast_to_scaffold", 
             "outputs": [
@@ -729,7 +880,13 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0", 
-            "tool_state": "{\"__page__\": 0, \"guideSequence\": \"null\", \"blast_tab\": \"null\", \"__rerun_remap_job_id__\": null, \"sequences\": \"null\"}", 
+            "tool_shed_repository": {
+                "changeset_revision": "3288cc5a57e5", 
+                "name": "blast_to_scaffold", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"__page__\": 0, \"guideSequence\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"blast_tab\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"sequences\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\"}", 
             "tool_version": "0.9.0", 
             "type": "tool", 
             "uuid": "4e68c3e8-b825-40bd-ae22-a74ca7048737", 
@@ -745,7 +902,12 @@
                     "output_name": "output"
                 }
             }, 
-            "inputs": [], 
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Regex Find And Replace", 
+                    "name": "input"
+                }
+            ], 
             "label": null, 
             "name": "Regex Find And Replace", 
             "outputs": [
@@ -769,7 +931,13 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0", 
-            "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"checks\": \"[{\\\"__index__\\\": 0, \\\"replacement\\\": \\\">Nora_MV\\\", \\\"pattern\\\": \\\">.+\\\"}]\", \"__page__\": 0}", 
+            "tool_shed_repository": {
+                "changeset_revision": "9ea374bb0350", 
+                "name": "regex_find_replace", 
+                "owner": "jjohnson", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
+            "tool_state": "{\"input\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null, \"checks\": \"[{\\\"__index__\\\": 0, \\\"replacement\\\": \\\">Nora_MV\\\", \\\"pattern\\\": \\\">.+\\\"}]\", \"__page__\": 0}", 
             "tool_version": "0.1.0", 
             "type": "tool", 
             "uuid": "d804abd4-ad4e-4382-a81d-b592bec797cf", 
@@ -782,5 +950,5 @@
             ]
         }
     }, 
-    "uuid": "6d905af0-243a-42b9-8951-a5477cfa6d88"
+    "uuid": "5c90686e-2dd0-43c4-bd64-a5ed21bcf2ff"
 }
\ No newline at end of file