changeset 2:48b020a0d2f7 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
author drosofff
date Fri, 13 May 2016 05:46:40 -0400
parents 3d8eb2c065c7
children ba15c770fd40
files Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-1.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-2.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-3.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-4.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-1.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-2.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-1.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-2.ga Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-3.ga Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_1-1,2,3.ga Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_2-1,2.ga repository_dependencies.xml
diffstat 12 files changed, 853 insertions(+), 97 deletions(-) [+]
line wrap: on
line diff
--- 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": [], 
             "position": {
-                "left": 211.9375, 
+                "left": 192.9375, 
                 "top": 200
             }, 
             "tool_errors": null, 
@@ -106,6 +106,12 @@
             }, 
             "tool_errors": null, 
             "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": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", 
-            "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\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"Nmode\": \"\\\"reject\\\"\"}", 
+            "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\\\"\"}", 
             "tool_version": "1.3.6", 
             "type": "tool", 
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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 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", 
-            "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"__workflow_invocation_uuid__\": \"\\\"ae5b2b58802911e5808df01fafdfc061\\\"\", \"title\": \"\\\"Blastn candidate database\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}", 
+            "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 @@
             }, 
             "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\\\": \\\"fasta2tabular\\\", \\\"__current_case__\\\": 0}\", \"__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__\\\": 0, \\\"conversionType\\\": \\\"fasta2tabular\\\"}\", \"__rerun_remap_job_id__\": null}", 
             "tool_version": "1.1.0", 
             "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 @@
             }, 
             "tool_errors": null, 
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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", 
             "uuid": "e22c6843-8125-49d6-9dcd-546155536f78", 
@@ -389,7 +465,7 @@
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         "9": {
             "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", 
+            "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_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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+                "owner": "devteam", 
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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_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\": \"null\", \"blast\": \"null\"}", 
+            "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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             "type": "tool", 
             "uuid": "84989771-81db-4d86-bff6-cfda892b1959", 
@@ -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 @@
             }, 
             "tool_errors": null, 
             "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, 
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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": "{\"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
--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-2.ga	Mon Apr 11 13:14:14 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-2.ga	Fri May 13 05:46:40 2016 -0400
@@ -106,6 +106,12 @@
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             "tool_errors": null, 
             "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", 
@@ -144,6 +150,12 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", 
+            "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\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"Nmode\": \"\\\"reject\\\"\"}", 
             "tool_version": "1.3.6", 
             "type": "tool", 
@@ -188,7 +200,13 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", 
-            "tool_state": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"input_file\": \"null\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"True\\\"\", \"tax\": \"{\\\"taxselect\\\": \\\"\\\", \\\"__current_case__\\\": 0}\", \"__workflow_invocation_uuid__\": \"\\\"ae5b2b58802911e5808df01fafdfc061\\\"\", \"title\": \"\\\"Blastn candidate database\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"parse_seqids\": \"\\\"False\\\"\"}", 
+            "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\": \"null\", \"input_file\": \"null\", \"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", 
@@ -233,6 +251,12 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", 
+            "tool_shed_repository": {
+                "changeset_revision": "201c568972c3", 
+                "name": "concatenate_multiple_datasets", 
+                "owner": "mvdbeek", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
             "tool_version": "0.2", 
             "type": "tool", 
@@ -291,6 +315,12 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", 
+            "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\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"dm6\\\", \\\"__current_case__\\\": 0}\", \"method\": \"\\\"k_option\\\"\"}", 
             "tool_version": "1.1.2", 
             "type": "tool", 
@@ -305,7 +335,7 @@
         }, 
         "7": {
             "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.5", 
             "id": 7, 
             "input_connections": {
                 "inputs_0|input": {
@@ -336,9 +366,15 @@
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             }, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/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"
+            }, 
             "tool_state": "{\"__page__\": 0, \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"end_hash_length\": \"\\\"29\\\"\", \"__rerun_remap_job_id__\": null, \"start_hash_length\": \"\\\"13\\\"\"}", 
-            "tool_version": "1.1.4", 
+            "tool_version": "1.1.5", 
             "type": "tool", 
             "uuid": "4290f9b9-2ea7-4634-a639-bc008f1eb90c", 
             "workflow_outputs": [
@@ -385,7 +421,13 @@
             }, 
             "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_optional_id_files_opts\\\": {\\\"adv_optional_id_files_opts_selector\\\": \\\"none\\\", \\\"__current_case__\\\": 0}, \\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"False\\\", \\\"filter_query\\\": \\\"True\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"False\\\", \\\"qcov_hsp_perc\\\": \\\"0.0\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"5\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"4dd2fde8802311e5bcddf01fafdfc061\\\"\", \"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_optional_id_files_opts\\\": {\\\"__current_case__\\\": 0, \\\"adv_optional_id_files_opts_selector\\\": \\\"none\\\"}, \\\"identity_cutoff\\\": \\\"0.0\\\", \\\"adv_opts_selector\\\": \\\"advanced\\\", \\\"ungapped\\\": \\\"false\\\", \\\"filter_query\\\": \\\"true\\\", \\\"word_size\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"parse_deflines\\\": \\\"false\\\", \\\"qcov_hsp_perc\\\": \\\"0.0\\\", \\\"strand\\\": \\\"-strand both\\\", \\\"max_hits\\\": \\\"5\\\"}\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"__workflow_invocation_uuid__\": \"\\\"4dd2fde8802311e5bcddf01fafdfc061\\\"\", \"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_version": "0.1.06", 
             "type": "tool", 
             "uuid": "bf30a0ad-4ef9-49f0-b4c7-4aae52017748", 
@@ -444,6 +486,12 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", 
+            "tool_shed_repository": {
+                "changeset_revision": "6dfa79a6908a", 
+                "name": "msp_blastparser_and_hits", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "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\": \"null\", \"blast\": \"null\"}", 
             "tool_version": "2.4.3", 
             "type": "tool", 
@@ -551,6 +599,12 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_cap3/cap3/1.2.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "ddb463fdf57e", 
+                "name": "msp_cap3", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "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_version": "1.2.0", 
             "type": "tool", 
@@ -599,6 +653,12 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", 
+            "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\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"blast_type\": \"\\\"blastn\\\"\", \"query\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
             "tool_version": "0.1.06", 
             "type": "tool", 
@@ -645,6 +705,12 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "3288cc5a57e5", 
+                "name": "blast_to_scaffold", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "tool_state": "{\"__page__\": 0, \"guideSequence\": \"null\", \"blast_tab\": \"null\", \"__rerun_remap_job_id__\": null, \"sequences\": \"null\"}", 
             "tool_version": "0.9.0", 
             "type": "tool", 
@@ -692,6 +758,12 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/jjohnson/regex_find_replace/regex1/0.1.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "9ea374bb0350", 
+                "name": "regex_find_replace", 
+                "owner": "jjohnson", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"checks\": \"[{\\\"__index__\\\": 0, \\\"replacement\\\": \\\">Nora_raw_reads\\\", \\\"pattern\\\": \\\">.+\\\"}]\", \"__page__\": 0}", 
             "tool_version": "0.1.0", 
             "type": "tool", 
--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-3.ga	Mon Apr 11 13:14:14 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-3.ga	Fri May 13 05:46:40 2016 -0400
@@ -106,6 +106,12 @@
             }, 
             "tool_errors": null, 
             "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", 
@@ -144,6 +150,12 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", 
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--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-4.ga	Mon Apr 11 13:14:14 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-4.ga	Fri May 13 05:46:40 2016 -0400
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--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-1.ga	Mon Apr 11 13:14:14 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-1.ga	Fri May 13 05:46:40 2016 -0400
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+                "name": "fetch_fasta_from_ncbi", 
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+                "changeset_revision": "3288cc5a57e5", 
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+                "owner": "drosofff", 
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--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-2.ga	Mon Apr 11 13:14:14 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-2.ga	Fri May 13 05:46:40 2016 -0400
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@@ -197,10 +203,16 @@
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+            "tool_shed_repository": {
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+                "name": "fastq_to_fasta", 
+                "owner": "devteam", 
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@@ -242,10 +254,16 @@
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@@ -280,7 +298,13 @@
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+                "name": "msp_fasta_tabular_converter", 
+                "owner": "drosofff", 
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+            "tool_shed_repository": {
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+                "name": "msp_fasta_tabular_converter", 
+                "owner": "drosofff", 
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@@ -350,10 +380,16 @@
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@@ -388,10 +424,16 @@
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+            "tool_shed_repository": {
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+                "name": "fasta_filter_by_length", 
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@@ -430,10 +472,16 @@
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+            "tool_shed_repository": {
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+                "name": "ncbi_blast_plus", 
+                "owner": "devteam", 
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-            "uuid": "None", 
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@@ -500,7 +548,13 @@
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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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--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-1.ga	Mon Apr 11 13:14:14 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-1.ga	Fri May 13 05:46:40 2016 -0400
@@ -100,6 +100,12 @@
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             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastq_to_fasta/cshl_fastq_to_fasta/1.0.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "186b8d913e6c", 
+                "name": "fastq_to_fasta", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
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@@ -145,6 +151,12 @@
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             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fastx_trimmer/cshl_fastx_trimmer/1.0.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "377ac2829eac", 
+                "name": "fastx_trimmer", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
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@@ -183,7 +195,13 @@
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+            "tool_shed_repository": {
+                "changeset_revision": "330dd8a8c31a", 
+                "name": "msp_fasta_tabular_converter", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
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+            "tool_state": "{\"__page__\": 0, \"switch\": \"{\\\"input\\\": null, \\\"__current_case__\\\": 0, \\\"conversionType\\\": \\\"fasta2tabular\\\"}\", \"__rerun_remap_job_id__\": null}", 
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+            "tool_shed_repository": {
+                "changeset_revision": "330dd8a8c31a", 
+                "name": "msp_fasta_tabular_converter", 
+                "owner": "drosofff", 
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@@ -290,6 +314,12 @@
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+            "tool_shed_repository": {
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+                "name": "msp_sr_bowtie", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
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@@ -351,6 +381,12 @@
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+            "tool_shed_repository": {
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+                "name": "msp_sr_bowtie", 
+                "owner": "drosofff", 
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@@ -391,6 +427,12 @@
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--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-2.ga	Mon Apr 11 13:14:14 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-2.ga	Fri May 13 05:46:40 2016 -0400
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--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-3.ga	Mon Apr 11 13:14:14 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-3.ga	Fri May 13 05:46:40 2016 -0400
@@ -111,6 +111,12 @@
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+            "tool_shed_repository": {
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+                "name": "fetch_fasta_from_ncbi", 
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@@ -293,6 +311,12 @@
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             "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"0\\\"\", \"additional_filters\": \"{\\\"filter_term_out\\\": \\\"Patent\\\", \\\"filter_relativeCov\\\": \\\"0.0\\\", \\\"filter_meanScore\\\": \\\"100.0\\\", \\\"use_filters\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"filter_term_in\\\": \\\"${target_virus}\\\", \\\"filter_maxScore\\\": \\\"0.0\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"short\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", 
             "tool_version": "2.4.3", 
             "type": "tool", 
@@ -496,6 +538,12 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", 
+            "tool_shed_repository": {
+                "changeset_revision": "201c568972c3", 
+                "name": "concatenate_multiple_datasets", 
+                "owner": "mvdbeek", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
             "tool_version": "0.2", 
             "type": "tool", 
@@ -544,6 +592,12 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.07", 
+            "tool_shed_repository": {
+                "changeset_revision": "7f3c448e119b", 
+                "name": "ncbi_blast_plus", 
+                "owner": "devteam", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "tool_state": "{\"evalue_cutoff\": \"\\\"0.001\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"blast_type\": \"\\\"blastn\\\"\", \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"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\\\"]}\", \"query\": \"null\"}", 
             "tool_version": "0.1.07", 
             "type": "tool", 
@@ -584,6 +638,12 @@
             "post_job_actions": {}, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/blast_to_scaffold/blast2scaffold/0.9.0", 
+            "tool_shed_repository": {
+                "changeset_revision": "3288cc5a57e5", 
+                "name": "blast_to_scaffold", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "tool_state": "{\"__page__\": 0, \"guideSequence\": \"null\", \"blast_tab\": \"null\", \"__rerun_remap_job_id__\": null, \"sequences\": \"null\"}", 
             "tool_version": "0.9.0", 
             "type": "tool", 
@@ -630,6 +690,12 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", 
+            "tool_shed_repository": {
+                "changeset_revision": "201c568972c3", 
+                "name": "concatenate_multiple_datasets", 
+                "owner": "mvdbeek", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
             "tool_version": "0.2", 
             "type": "tool", 
--- a/Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_1-1,2,3.ga	Mon Apr 11 13:14:14 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_1-1,2,3.ga	Fri May 13 05:46:40 2016 -0400
@@ -27,7 +27,7 @@
             "tool_state": "{\"collection_type\": \"list\", \"name\": \"Read fastq files\"}", 
             "tool_version": null, 
             "type": "data_collection_input", 
-            "uuid": "None", 
+            "uuid": "ca202c6a-46b7-4f3a-a2ab-dbc781f331b7", 
             "workflow_outputs": [
                 {
                     "label": null, 
@@ -59,7 +59,7 @@
             "tool_state": "{\"collection_type\": \"list\", \"name\": \"Nora Virus Genomes\"}", 
             "tool_version": null, 
             "type": "data_collection_input", 
-            "uuid": "None", 
+            "uuid": "e8e196c7-c854-4bd9-ace2-345a0d797090", 
             "workflow_outputs": [
                 {
                     "label": null, 
@@ -100,10 +100,16 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", 
+            "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, \"clip_source\": \"{\\\"clip_source_list\\\": \\\"prebuilt\\\", \\\"clip_sequence\\\": \\\"CTGTAGGCACCATCAATCGT\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"Nmode\": \"\\\"reject\\\"\"}", 
             "tool_version": "1.3.6", 
             "type": "tool", 
-            "uuid": "None", 
+            "uuid": "afa187ce-544c-4287-8699-a9efe8ce45ab", 
             "workflow_outputs": []
         }, 
         "3": {
@@ -145,10 +151,16 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", 
+            "tool_shed_repository": {
+                "changeset_revision": "201c568972c3", 
+                "name": "concatenate_multiple_datasets", 
+                "owner": "mvdbeek", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
             "tool_version": "0.2", 
             "type": "tool", 
-            "uuid": "None", 
+            "uuid": "73d5e37a-8a61-4bab-8bf5-12b12fc45988", 
             "workflow_outputs": []
         }, 
         "4": {
@@ -197,10 +209,16 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", 
+            "tool_shed_repository": {
+                "changeset_revision": "201c568972c3", 
+                "name": "concatenate_multiple_datasets", 
+                "owner": "mvdbeek", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
             "tool_version": "0.2", 
             "type": "tool", 
-            "uuid": "None", 
+            "uuid": "f15e8add-3a18-4607-b5e2-51448dcdeb77", 
             "workflow_outputs": []
         }, 
         "5": {
@@ -257,10 +275,16 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", 
+            "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\": \"\\\"No\\\"\", \"v_mismatches\": \"\\\"0\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"method\": \"\\\"multiple\\\"\"}", 
             "tool_version": "1.1.2", 
             "type": "tool", 
-            "uuid": "None", 
+            "uuid": "a9880e4e-f47f-4a21-ad20-5aefb83b57ad", 
             "workflow_outputs": []
         }, 
         "6": {
@@ -309,10 +333,16 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", 
+            "tool_shed_repository": {
+                "changeset_revision": "201c568972c3", 
+                "name": "concatenate_multiple_datasets", 
+                "owner": "mvdbeek", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
             "tool_version": "0.2", 
             "type": "tool", 
-            "uuid": "None", 
+            "uuid": "afeb8258-2959-4b81-bec4-aaa342dd930d", 
             "workflow_outputs": []
         }, 
         "7": {
@@ -349,10 +379,10 @@
             }, 
             "tool_errors": null, 
             "tool_id": "wc_gnu", 
-            "tool_state": "{\"__page__\": 0, \"include_header\": \"\\\"True\\\"\", \"input1\": \"null\", \"options\": \"[\\\"lines\\\"]\", \"__rerun_remap_job_id__\": null}", 
+            "tool_state": "{\"__page__\": 0, \"include_header\": \"\\\"true\\\"\", \"input1\": \"null\", \"options\": \"[\\\"lines\\\"]\", \"__rerun_remap_job_id__\": null}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
-            "uuid": "None", 
+            "uuid": "98092466-d430-48bd-b285-770aeee41153", 
             "workflow_outputs": [
                 {
                     "label": null, 
@@ -418,6 +448,12 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.1.5", 
+            "tool_shed_repository": {
+                "changeset_revision": "68f58363f1c6", 
+                "name": "msp_sr_readmap_and_size_histograms", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "tool_state": "{\"minquery\": \"\\\"18\\\"\", \"__page__\": 0, \"rows_per_page\": \"\\\"8\\\"\", \"yrange\": \"\\\"0\\\"\", \"title\": \"\\\"Readmaps and size distributions\\\"\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"series\\\": [{\\\"__index__\\\": 0, \\\"norm\\\": \\\"1.0\\\", \\\"input\\\": null}], \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"maxquery\": \"\\\"30\\\"\", \"xlabel\": \"\\\"Coordinates/read size\\\"\", \"ylabel\": \"\\\"Number of reads\\\"\", \"gff\": \"null\"}", 
             "tool_version": "1.1.5", 
             "type": "tool", 
--- a/Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_2-1,2.ga	Mon Apr 11 13:14:14 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_remapping_in_Use_Cases_2-1,2.ga	Fri May 13 05:46:40 2016 -0400
@@ -27,7 +27,7 @@
             "tool_state": "{\"collection_type\": \"list\", \"name\": \"Small Read fastq files\"}", 
             "tool_version": null, 
             "type": "data_collection_input", 
-            "uuid": "None", 
+            "uuid": "35d6ef0f-98d0-439a-aef4-3d4d2c85e309", 
             "workflow_outputs": [
                 {
                     "label": null, 
@@ -100,10 +100,16 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", 
+            "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, \"clip_source\": \"{\\\"clip_source_list\\\": \\\"prebuilt\\\", \\\"clip_sequence\\\": \\\"TGGAATTCTCGGGTGCCAAG\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"Nmode\": \"\\\"reject\\\"\"}", 
             "tool_version": "1.3.6", 
             "type": "tool", 
-            "uuid": "None", 
+            "uuid": "4d773707-d5ed-48c2-b9d2-334f32e2e1f7", 
             "workflow_outputs": []
         }, 
         "3": {
@@ -152,10 +158,16 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/mvdbeek/concatenate_multiple_datasets/cat_multiple/0.2", 
+            "tool_shed_repository": {
+                "changeset_revision": "201c568972c3", 
+                "name": "concatenate_multiple_datasets", 
+                "owner": "mvdbeek", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "tool_state": "{\"input\": \"null\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", 
             "tool_version": "0.2", 
             "type": "tool", 
-            "uuid": "None", 
+            "uuid": "c1d6a090-fc9b-4957-a952-4241216e082a", 
             "workflow_outputs": []
         }, 
         "4": {
@@ -212,10 +224,16 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", 
+            "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\": \"\\\"No\\\"\", \"v_mismatches\": \"\\\"0\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"method\": \"\\\"multiple\\\"\"}", 
             "tool_version": "1.1.2", 
             "type": "tool", 
-            "uuid": "None", 
+            "uuid": "7c3b7910-0490-4b69-ad32-c4ab81d01046", 
             "workflow_outputs": []
         }, 
         "5": {
@@ -252,10 +270,10 @@
             }, 
             "tool_errors": null, 
             "tool_id": "wc_gnu", 
-            "tool_state": "{\"__page__\": 0, \"include_header\": \"\\\"True\\\"\", \"input1\": \"null\", \"options\": \"[\\\"lines\\\"]\", \"__rerun_remap_job_id__\": null}", 
+            "tool_state": "{\"__page__\": 0, \"include_header\": \"\\\"true\\\"\", \"input1\": \"null\", \"options\": \"[\\\"lines\\\"]\", \"__rerun_remap_job_id__\": null}", 
             "tool_version": "1.0.0", 
             "type": "tool", 
-            "uuid": "None", 
+            "uuid": "5967713a-0548-48b9-a675-227ad48b420c", 
             "workflow_outputs": [
                 {
                     "label": null, 
@@ -321,6 +339,12 @@
             }, 
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_readmap_and_size_histograms/Readmap/1.1.5", 
+            "tool_shed_repository": {
+                "changeset_revision": "68f58363f1c6", 
+                "name": "msp_sr_readmap_and_size_histograms", 
+                "owner": "drosofff", 
+                "tool_shed": "toolshed.g2.bx.psu.edu"
+            }, 
             "tool_state": "{\"minquery\": \"\\\"18\\\"\", \"__page__\": 0, \"rows_per_page\": \"\\\"8\\\"\", \"yrange\": \"\\\"0\\\"\", \"title\": \"\\\"Readmaps and size distributions\\\"\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"series\\\": [{\\\"__index__\\\": 0, \\\"norm\\\": \\\"1.0\\\", \\\"input\\\": null}], \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"__rerun_remap_job_id__\": null, \"maxquery\": \"\\\"30\\\"\", \"xlabel\": \"\\\"Coordinates/read size\\\"\", \"ylabel\": \"\\\"Number of reads\\\"\", \"gff\": \"null\"}", 
             "tool_version": "1.1.5", 
             "type": "tool", 
--- a/repository_dependencies.xml	Mon Apr 11 13:14:14 2016 -0400
+++ b/repository_dependencies.xml	Fri May 13 05:46:40 2016 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="These workflows require the repository suite_metavisitor_1_2">
-    <repository changeset_revision="e24919521ffb" name="suite_metavisitor_1_2" owner="drosofff" toolshed="http://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="0f33d75ae19b" name="suite_metavisitor_1_2" owner="drosofff" toolshed="http://toolshed.g2.bx.psu.edu" />
 </repositories>