diff Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-4.ga @ 3:ba15c770fd40 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4

--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-4.ga	Fri May 13 05:46:40 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_1-4.ga	Thu Nov 17 07:27:04 2016 -0500
@@ -95,7 +95,7 @@
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/yac_clipper/yac/1.3.6", 
             "tool_shed_repository": {
-                "changeset_revision": "91cce7c1436d", 
+                "changeset_revision": "a18edcf9c7ed", 
                 "name": "yac_clipper", 
                 "owner": "drosofff", 
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -196,7 +196,7 @@
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", 
             "tool_shed_repository": {
-                "changeset_revision": "330dd8a8c31a", 
+                "changeset_revision": "36388b666bfc", 
                 "name": "msp_fasta_tabular_converter", 
                 "owner": "drosofff", 
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -242,7 +242,7 @@
             "tool_errors": null, 
             "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_fasta_tabular_converter/fasta_tabular_converter/1.1.0", 
             "tool_shed_repository": {
-                "changeset_revision": "330dd8a8c31a", 
+                "changeset_revision": "36388b666bfc", 
                 "name": "msp_fasta_tabular_converter", 
                 "owner": "drosofff", 
                 "tool_shed": "toolshed.g2.bx.psu.edu"
@@ -261,7 +261,7 @@
         }, 
         "6": {
             "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1", 
             "id": 6, 
             "input_connections": {
                 "input": {
@@ -310,15 +310,15 @@
                 }
             }, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/drosofff/msp_sr_bowtie/bowtieForSmallRNA/1.1.2.1", 
             "tool_shed_repository": {
-                "changeset_revision": "c1bfa227bbb6", 
+                "changeset_revision": "615d2550977f", 
                 "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", 
+            "tool_version": "1.1.2.1", 
             "type": "tool", 
             "uuid": "e22c6843-8125-49d6-9dcd-546155536f78", 
             "workflow_outputs": [
@@ -331,7 +331,7 @@
         }, 
         "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": {
@@ -362,15 +362,15 @@
                 }
             }, 
             "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": "f08d9c814ffb", 
+                "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": [
@@ -383,7 +383,7 @@
         }, 
         "8": {
             "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08", 
             "id": 8, 
             "input_connections": {
                 "db_opts|histdb": {
@@ -410,15 +410,15 @@
             }, 
             "post_job_actions": {}, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.06", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.1.08", 
             "tool_shed_repository": {
-                "changeset_revision": "577d9c12411a", 
+                "changeset_revision": "3034ce97dd33", 
                 "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", 
+            "tool_version": "0.1.08", 
             "type": "tool", 
             "uuid": "bf30a0ad-4ef9-49f0-b4c7-4aae52017748", 
             "workflow_outputs": [
@@ -488,7 +488,7 @@
             "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", 
+                "changeset_revision": "1991c830504a", 
                 "name": "msp_blastparser_and_hits", 
                 "owner": "drosofff", 
                 "tool_shed": "toolshed.g2.bx.psu.edu"