Mercurial > repos > drosofff > metavisitor_workflows
changeset 2:48b020a0d2f7 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
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--- 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", "uuid": "69611c78-3f25-4471-abf7-426ec35fd2db", @@ -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, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", - "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_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\\\"\"}", "tool_version": "1.1.2", "type": "tool", "uuid": "e22c6843-8125-49d6-9dcd-546155536f78", @@ -389,7 +465,7 @@ }, "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": { "inputs_0|input": { @@ -420,9 +496,15 @@ } }, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", - "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_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\\\": {\\\"__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 @@ }, "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\\\": {\\\"__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": "bf30a0ad-4ef9-49f0-b4c7-4aae52017748", @@ -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 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", - "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" + }, + "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\\\"}\"}", "tool_version": "2.4.3", "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 @@ }, "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
--- 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 @@ }, "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 @@ } }, "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", + "tool_shed_repository": { + "changeset_revision": "91cce7c1436d", + "name": "yac_clipper", + "owner": "drosofff", + "tool_shed": "toolshed.g2.bx.psu.edu" + 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"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", @@ -401,6 +437,12 @@ }, "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", @@ -447,6 +489,12 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", + "tool_shed_repository": { + "changeset_revision": "f08d9c814ffb", + "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", "type": "tool", @@ -495,7 +543,13 @@ }, "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, 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"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", @@ -661,6 +721,12 @@ }, "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, 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[\\\"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", @@ -755,6 +827,12 @@ }, "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", @@ -802,6 +880,12 @@ }, "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_Median-Norm-reads\\\", \\\"pattern\\\": \\\">.+\\\"}]\", \"__page__\": 0}", "tool_version": "0.1.0", "type": "tool",
--- 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 @@ -94,6 +94,12 @@ "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", @@ -145,6 +151,12 @@ }, "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", @@ -183,7 +195,13 @@ }, "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\\\": null, \\\"__current_case__\\\": 0, \\\"conversionType\\\": \\\"fasta2tabular\\\"}\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.0", "type": "tool", "uuid": "c700f2a8-231e-4792-a0cc-0e542d36b414", @@ -223,7 +241,13 @@ }, "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\\\": null, \\\"__current_case__\\\": 2, \\\"conversionType\\\": \\\"tabular2fastaweight\\\"}\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.0", "type": "tool", "uuid": "a51f4a8a-2bea-4fc8-97a5-97af74cd4144", @@ -287,6 +311,12 @@ }, "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", @@ -333,6 +363,12 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", + "tool_shed_repository": { + "changeset_revision": "f08d9c814ffb", + "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", "type": "tool", @@ -375,7 +411,13 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", - 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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 @@ -27,7 +27,7 @@ "tool_state": "{\"collection_type\": \"list\", \"name\": \"Input Dataset Collection\"}", "tool_version": null, "type": "data_collection_input", - "uuid": "None", + "uuid": "6624e038-53b9-47b7-8408-36c8721e7530", "workflow_outputs": [ { "label": null, @@ -70,7 +70,7 @@ }, "2": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.3", + "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.4", "id": 2, "input_connections": {}, "inputs": [], @@ -110,11 +110,17 @@ } }, "tool_errors": null, - "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/fetch_fasta_from_ncbi/retrieve_fasta_from_NCBI/0.9.3", + "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\": \"\\\"NC_001834.1\\\"\", \"dbname\": \"\\\"nuccore\\\"\"}", - "tool_version": "0.9.3", + "tool_version": "0.9.4", "type": "tool", - "uuid": "None", + "uuid": "61626aa3-06cc-43e6-baa7-40cef265dba9", "workflow_outputs": [] }, "3": { @@ -149,10 +155,16 @@ }, "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\": \"\\\"50\\\"\", \"__rerun_remap_job_id__\": null, \"clip_source\": \"{\\\"clip_source_list\\\": \\\"prebuilt\\\", \\\"clip_sequence\\\": \\\"TGGAATTCTCGGGTGCCAAG\\\", \\\"__current_case__\\\": 0}\", \"input\": \"null\", \"Nmode\": \"\\\"accept\\\"\"}", "tool_version": "1.3.6", "type": "tool", - "uuid": "None", + "uuid": "690762cc-4e7a-4ac7-a9ef-c21fda4a83b7", "workflow_outputs": [] }, "4": { @@ -187,10 +199,16 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", - 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"uuid": "None", + "uuid": "d6eb4143-09ca-4822-a5c9-940b1abed975", "workflow_outputs": [] }, "6": { @@ -270,7 +294,13 @@ }, "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\\\": null, \\\"__current_case__\\\": 0, \\\"conversionType\\\": \\\"fasta2tabular\\\"}\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.0", "type": "tool", "uuid": "890947a5-b6c3-4905-9659-9f4cb58ae3de", @@ -310,7 +340,13 @@ }, "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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"uuid": "None", + "uuid": "a056b1c2-cf05-459e-8532-3d1548b268cf", "workflow_outputs": [ { "label": null, @@ -443,10 +485,16 @@ }, "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\": \"\\\"unal\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"method\": \"\\\"k_option\\\"\"}", "tool_version": "1.1.2", "type": "tool", - "uuid": "None", + "uuid": "749b801a-afe6-4a36-b13a-30de5d736a92", "workflow_outputs": [] }, "10": { @@ -506,10 +554,16 @@ }, "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\": \"\\\"unal\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"method\": \"\\\"k_option\\\"\"}", "tool_version": "1.1.2", "type": "tool", - "uuid": "None", + "uuid": "ff1dd365-8697-42f6-bad7-81ee0ec61e3e", "workflow_outputs": [] }, "11": { @@ -546,10 +600,16 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", + "tool_shed_repository": { + "changeset_revision": "f08d9c814ffb", + "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", "type": "tool", - "uuid": "None", + "uuid": "a9ea9af5-d524-4f62-8969-70cbc5be79dd", "workflow_outputs": [ { "label": null, @@ -588,10 +648,16 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_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\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query\": \"null\", \"query_gencode\": \"\\\"1\\\"\", \"blast_type\": \"\\\"blastx\\\"\", \"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\\\"]}\"}", "tool_version": "0.1.06", "type": "tool", - "uuid": "None", + "uuid": "b9891d9f-e295-4ffd-aa8e-a8c8f76efe59", "workflow_outputs": [ { "label": null, @@ -653,7 +719,13 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", - "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"use_filters\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"verbose\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", + "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\": \"{\\\"__current_case__\\\": 0, \\\"use_filters\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"verbose\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", "tool_version": "2.4.3", "type": "tool", "uuid": "32401021-0c03-4c16-a8a3-b08c54d34ce5", @@ -702,10 +774,16 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/cherry_pick_fasta/cherry_pick_fasta/0.9.0", + "tool_shed_repository": { + "changeset_revision": "c7a0ec8263b4", + "name": "cherry_pick_fasta", + "owner": "drosofff", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"query\": \"\\\"Drosophila_C_virus\\\"\"}", "tool_version": "0.9.0", "type": "tool", - "uuid": "None", + "uuid": "392efdea-8e0e-4bd2-952a-03e1fb231996", "workflow_outputs": [] }, "15": { @@ -740,10 +818,16 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/cherry_pick_fasta/cherry_pick_fasta/0.9.0", + "tool_shed_repository": { + "changeset_revision": "c7a0ec8263b4", + "name": "cherry_pick_fasta", + "owner": "drosofff", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"query\": \"\\\"Cricket_paralysis_virus\\\"\"}", "tool_version": "0.9.0", "type": "tool", - "uuid": "None", + "uuid": "8a5da6c1-578b-4cc1-8021-163530d28a62", "workflow_outputs": [] }, "16": { @@ -787,7 +871,7 @@ "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}", "tool_version": "1.0.0", "type": "tool", - "uuid": "None", + "uuid": "9301a6e7-685b-4bb1-b13d-73353d438526", "workflow_outputs": [ { "label": null, @@ -893,10 +977,16 @@ }, "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": "{\"overlapidentity\": \"\\\"90\\\"\", \"inputSequences\": \"null\", \"__rerun_remap_job_id__\": null, \"overlaplength\": \"\\\"40\\\"\", \"__page__\": 0}", "tool_version": "1.2.0", "type": "tool", - "uuid": "None", + "uuid": "fda8ab76-affc-46d2-997f-09cfe13e54fd", "workflow_outputs": [ { "label": null, @@ -935,10 +1025,16 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_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\\\"\", \"__page__\": 0, \"adv_opts\": \"{\\\"adv_opts_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query_gencode\": \"\\\"1\\\"\", \"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": "0.1.06", "type": "tool", - "uuid": "None", + "uuid": "43f3188c-43ca-41a0-9918-38fc03977321", "workflow_outputs": [ { "label": null, @@ -989,6 +1085,12 @@ }, "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",
--- 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 @@ -159,7 +159,13 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"False\\\", \\\"unaligned_file\\\": \\\"True\\\", \\\"type\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_1\\\": null}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"AgamP4\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"False\\\"\", \"analysis_type\": \"{\\\"alignment_options\\\": {\\\"alignment_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"effort_options\\\": {\\\"effort_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"sam_options\\\": {\\\"sam_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"other_options\\\": {\\\"other_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"reporting_options\\\": {\\\"k\\\": \\\"1\\\", \\\"reporting_options_selector\\\": \\\"k\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"sam_opt\\\": \\\"True\\\", \\\"input_options\\\": {\\\"int_quals\\\": \\\"False\\\", \\\"solexa_quals\\\": \\\"False\\\", \\\"skip\\\": \\\"0\\\", \\\"input_options_selector\\\": \\\"yes\\\", \\\"qv_encoding\\\": \\\"--phred33\\\", \\\"__current_case__\\\": 0, \\\"trim3\\\": \\\"20\\\", \\\"qupto\\\": \\\"100000000\\\", \\\"trim5\\\": \\\"0\\\"}}\"}", + "tool_shed_repository": { + "changeset_revision": "a9d4f71dbfb0", + "name": "bowtie2", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"false\\\", \\\"unaligned_file\\\": \\\"true\\\", \\\"type\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_1\\\": null}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"AgamP4\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"false\\\"\", \"analysis_type\": \"{\\\"alignment_options\\\": {\\\"__current_case__\\\": 1, \\\"alignment_options_selector\\\": \\\"no\\\"}, \\\"effort_options\\\": {\\\"effort_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"sam_options\\\": {\\\"sam_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"other_options\\\": {\\\"other_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"reporting_options\\\": {\\\"k\\\": \\\"1\\\", \\\"reporting_options_selector\\\": \\\"k\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"sam_opt\\\": \\\"true\\\", \\\"input_options\\\": {\\\"int_quals\\\": \\\"false\\\", \\\"solexa_quals\\\": \\\"false\\\", \\\"skip\\\": \\\"0\\\", \\\"input_options_selector\\\": \\\"yes\\\", \\\"qv_encoding\\\": \\\"--phred33\\\", \\\"__current_case__\\\": 0, \\\"trim3\\\": \\\"20\\\", \\\"qupto\\\": \\\"100000000\\\", \\\"trim5\\\": \\\"0\\\"}}\"}", "tool_version": "2.2.6.2", "type": "tool", "uuid": "15edcf5f-9b38-4b7e-ad04-f816d1d4d126", @@ -197,10 +203,16 @@ }, "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" + }, "tool_state": "{\"__page__\": 0, \"RENAMESEQ\": \"\\\"-r\\\"\", \"SKIPN\": \"\\\"\\\"\", \"input\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.0.0", "type": "tool", - "uuid": "None", + "uuid": "71496d9a-5490-46a7-930d-37ec45d1ccb8", "workflow_outputs": [] }, "4": { @@ -242,10 +254,16 @@ }, "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": "26ef2a8f-e79e-4e04-92d7-7629b56a3765", "workflow_outputs": [] }, "5": { @@ -280,7 +298,13 @@ }, "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\\\": null, \\\"__current_case__\\\": 0, \\\"conversionType\\\": \\\"fasta2tabular\\\"}\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.0", "type": "tool", "uuid": "1d78a822-0e08-4e92-a9f7-bc80166e36a1", @@ -318,7 +342,13 @@ }, "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\\\": null, \\\"__current_case__\\\": 2, \\\"conversionType\\\": \\\"tabular2fastaweight\\\"}\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.0", "type": "tool", "uuid": "d6d8e36c-641a-4662-b615-0745b9d9fb55", @@ -350,10 +380,16 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_oases/oasesoptimiserv/1.1.4", + "tool_shed_repository": { + "changeset_revision": "f08d9c814ffb", + "name": "msp_oases", + "owner": "drosofff", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, "tool_state": "{\"__page__\": 0, \"end_hash_length\": \"\\\"69\\\"\", \"inputs\": \"[{\\\"__index__\\\": 0, \\\"input\\\": null}]\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"start_hash_length\": \"\\\"25\\\"\"}", "tool_version": "1.1.4", "type": "tool", - "uuid": "None", + "uuid": "98ece8ec-729a-41a1-a61e-f6fcfce0e835", "workflow_outputs": [ { "label": null, @@ -388,10 +424,16 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/fasta_filter_by_length/fasta_filter_by_length/1.1", + "tool_shed_repository": { + "changeset_revision": "c8cd0a03db49", + "name": "fasta_filter_by_length", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"max_length\": \"\\\"0\\\"\", \"min_length\": \"\\\"5000\\\"\"}", "tool_version": "1.1", "type": "tool", - "uuid": "None", + "uuid": "db1f7d30-3b47-4030-9724-e371e0ec54a1", "workflow_outputs": [ { "label": null, @@ -430,10 +472,16 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_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, \"db_opts\": \"{\\\"db_opts_selector\\\": \\\"histdb\\\", \\\"subject\\\": \\\"\\\", \\\"histdb\\\": null, \\\"__current_case__\\\": 1, \\\"database\\\": \\\"\\\"}\", \"query_gencode\": \"\\\"1\\\"\", \"blast_type\": \"\\\"blastx\\\"\", \"query\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", "tool_version": "0.1.06", "type": "tool", - "uuid": "None", + "uuid": "b151f8e8-c81b-466a-8a31-d4b42d4b95e9", "workflow_outputs": [ { "label": null, @@ -500,7 +548,13 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_blastparser_and_hits/BlastParser_and_hits/2.4.3", - "tool_state": "{\"__page__\": 0, \"flanking\": \"\\\"5\\\"\", \"additional_filters\": \"{\\\"use_filters\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"verbose\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", + "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\": \"{\\\"__current_case__\\\": 0, \\\"use_filters\\\": \\\"no\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"verbose\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", "tool_version": "2.4.3", "type": "tool", "uuid": "30288e33-ff64-4089-9b45-428027744176",
--- 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 @@ }, "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" + }, "tool_state": "{\"input\": \"null\", \"RENAMESEQ\": \"\\\"-r\\\"\", \"SKIPN\": \"\\\"-n\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}", "tool_version": "1.0.0", "type": "tool", @@ -145,6 +151,12 @@ }, "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" + }, "tool_state": "{\"__page__\": 0, \"input\": \"null\", \"__rerun_remap_job_id__\": null, \"last\": \"\\\"27\\\"\", \"first\": \"\\\"1\\\"\"}", "tool_version": "1.0.0", "type": "tool", @@ -183,7 +195,13 @@ }, "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\\\": null, \\\"__current_case__\\\": 0, \\\"conversionType\\\": \\\"fasta2tabular\\\"}\", \"__rerun_remap_job_id__\": null}", "tool_version": "1.1.0", "type": "tool", "uuid": "7c179cc4-e0a4-4e8a-be6f-c445d70c721e", @@ -223,7 +241,13 @@ }, "tool_errors": 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"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\\\": \\\"hg19\\\", \\\"__current_case__\\\": 0}\", \"method\": \"\\\"k_option\\\"\"}", "tool_version": "1.1.2", "type": "tool", @@ -351,6 +381,12 @@ }, "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\": \"\\\"al\\\"\", \"v_mismatches\": \"\\\"2\\\"\", \"__rerun_remap_job_id__\": null, \"input\": \"null\", \"refGenomeSource\": 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"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", @@ -516,6 +564,12 @@ }, "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\\\": \\\"Patent\\\", \\\"filter_relativeCov\\\": \\\"0.0\\\", \\\"filter_meanScore\\\": \\\"0.0\\\", \\\"use_filters\\\": \\\"yes\\\", \\\"__current_case__\\\": 1, \\\"filter_term_in\\\": \\\"\\\", \\\"filter_maxScore\\\": \\\"0.0\\\"}\", \"__rerun_remap_job_id__\": null, \"mode\": \"\\\"short\\\"\", \"sequences\": \"null\", \"blast\": \"null\"}", "tool_version": "2.4.3", "type": "tool", @@ -562,6 +616,12 @@ }, "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_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 @@ -154,7 +154,13 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"False\\\", \\\"unaligned_file\\\": \\\"True\\\", \\\"type\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_1\\\": null}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"hg19\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"False\\\"\", \"analysis_type\": \"{\\\"alignment_options\\\": {\\\"alignment_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"effort_options\\\": {\\\"effort_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"sam_options\\\": {\\\"sam_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"other_options\\\": {\\\"other_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"reporting_options\\\": {\\\"k\\\": \\\"1\\\", \\\"reporting_options_selector\\\": \\\"k\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"sam_opt\\\": \\\"True\\\", \\\"input_options\\\": {\\\"input_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}}\"}", + "tool_shed_repository": { + "changeset_revision": "a9d4f71dbfb0", + "name": "bowtie2", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"false\\\", \\\"unaligned_file\\\": \\\"true\\\", \\\"type\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_1\\\": null}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"hg19\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"false\\\"\", \"analysis_type\": \"{\\\"alignment_options\\\": {\\\"__current_case__\\\": 1, \\\"alignment_options_selector\\\": \\\"no\\\"}, \\\"effort_options\\\": {\\\"effort_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"sam_options\\\": {\\\"sam_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"other_options\\\": {\\\"other_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"reporting_options\\\": {\\\"k\\\": \\\"1\\\", \\\"reporting_options_selector\\\": \\\"k\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"sam_opt\\\": \\\"true\\\", \\\"input_options\\\": {\\\"input_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}}\"}", "tool_version": "2.2.6.2", "type": "tool", "uuid": "76fe9f4e-cf0b-4480-aadf-ba461c595414", @@ -259,7 +265,13 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2", - 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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 @@ }, "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\": \"\\\"${reference_virus}\\\"\", \"dbname\": \"\\\"nuccore\\\"\"}", "tool_version": "0.9.4", "type": "tool", @@ -208,7 +214,13 @@ }, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.2.6.2", - "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"True\\\", \\\"unaligned_file\\\": \\\"False\\\", \\\"type\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_1\\\": null}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"vir1\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"False\\\"\", \"analysis_type\": \"{\\\"alignment_options\\\": {\\\"alignment_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"effort_options\\\": {\\\"effort_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"sam_options\\\": {\\\"sam_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"other_options\\\": {\\\"other_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"reporting_options\\\": {\\\"k\\\": \\\"1\\\", \\\"reporting_options_selector\\\": \\\"k\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"sam_opt\\\": \\\"True\\\", \\\"input_options\\\": {\\\"input_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}}\"}", + "tool_shed_repository": { + "changeset_revision": "a9d4f71dbfb0", + "name": "bowtie2", + "owner": "devteam", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, + "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"library\": \"{\\\"aligned_file\\\": \\\"true\\\", \\\"unaligned_file\\\": \\\"false\\\", \\\"type\\\": \\\"single\\\", \\\"__current_case__\\\": 0, \\\"input_1\\\": null}\", \"reference_genome\": \"{\\\"source\\\": \\\"indexed\\\", \\\"__current_case__\\\": 0, \\\"index\\\": \\\"vir1\\\"}\", \"rg\": \"{\\\"rg_selector\\\": \\\"do_not_set\\\", \\\"__current_case__\\\": 3}\", \"save_mapping_stats\": \"\\\"false\\\"\", \"analysis_type\": \"{\\\"alignment_options\\\": {\\\"__current_case__\\\": 1, \\\"alignment_options_selector\\\": \\\"no\\\"}, \\\"effort_options\\\": {\\\"effort_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"sam_options\\\": {\\\"sam_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"other_options\\\": {\\\"other_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"scoring_options\\\": {\\\"scoring_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}, \\\"analysis_type_selector\\\": \\\"full\\\", \\\"reporting_options\\\": {\\\"k\\\": \\\"1\\\", \\\"reporting_options_selector\\\": \\\"k\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"sam_opt\\\": \\\"true\\\", \\\"input_options\\\": {\\\"input_options_selector\\\": \\\"no\\\", \\\"__current_case__\\\": 1}}\"}", "tool_version": "2.2.6.2", "type": "tool", "uuid": "d8ac3b32-882b-4761-affd-b3f71ddb3fcb", @@ -240,7 +252,13 @@ "post_job_actions": {}, "tool_errors": null, "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.07", - "tool_state": "{\"__page__\": 0, 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"tool_id": "toolshed.g2.bx.psu.edu/repos/anmoljh/trinityrnaseq/trinityrnaseq/r20140717", + "tool_shed_repository": { + "changeset_revision": "0a576a57a9eb", + "name": "trinityrnaseq", + "owner": "anmoljh", + "tool_shed": "toolshed.g2.bx.psu.edu" + }, "tool_state": "{\"__page__\": 0, \"JM\": \"\\\"1G\\\"\", \"__rerun_remap_job_id__\": null, \"additional_params\": \"{\\\"use_additional\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"inputs\": \"{\\\"paired_or_single\\\": \\\"single\\\", \\\"input\\\": null, \\\"path_reinforcement_distance\\\": \\\"40\\\", \\\"__current_case__\\\": 1, \\\"library_type\\\": \\\"None\\\"}\"}", "tool_version": "r20140717", "type": "tool", @@ -331,6 +355,12 @@ }, "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\\\": \\\">\\\\\\\\1\\\", \\\"pattern\\\": \\\">(.+) len=.+\\\"}]\", \"__page__\": 0}", "tool_version": "0.1.0", "type": "tool", @@ -375,6 +405,12 @@ }, "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", @@ -445,6 +481,12 @@ }, "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\": \"\\\"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>