diff Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-1.ga @ 3:ba15c770fd40 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit 9e3f79e20670526453bbed9f5b028aabb1bb7ae4
author drosofff
date Thu, 17 Nov 2016 07:27:04 -0500
parents 48b020a0d2f7
children 46614c7dd247
line wrap: on
line diff
--- a/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-1.ga	Fri May 13 05:46:40 2016 -0400
+++ b/Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_2-1.ga	Thu Nov 17 07:27:04 2016 -0500
@@ -169,7 +169,7 @@
         }, 
         "4": {
             "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.08", 
             "id": 4, 
             "input_connections": {
                 "input_file": {
@@ -198,15 +198,15 @@
                 }
             }, 
             "tool_errors": null, 
-            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.06", 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/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": "{\"__page__\": 0, \"mask_data_file\": \"null\", \"title\": \"\\\"DCV NC_001834.1\\\"\", \"dbtype\": \"\\\"nucl\\\"\", \"__rerun_remap_job_id__\": null, \"hash_index\": \"\\\"true\\\"\", \"tax\": \"{\\\"__current_case__\\\": 0, \\\"taxselect\\\": \\\"\\\"}\", \"input_file\": \"null\", \"parse_seqids\": \"\\\"false\\\"\"}", 
-            "tool_version": "0.1.06", 
+            "tool_version": "0.1.08", 
             "type": "tool", 
             "uuid": "934e8c0a-4dfc-41ad-9d1b-efe9748389d9", 
             "workflow_outputs": []
@@ -409,15 +409,15 @@
                 }
             }, 
             "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\\\": \\\"AgamP4\\\", \\\"__current_case__\\\": 0}\", \"method\": \"\\\"k_option\\\"\"}", 
-            "tool_version": "1.1.2", 
+            "tool_version": "1.1.2.1", 
             "type": "tool", 
             "uuid": "a056b1c2-cf05-459e-8532-3d1548b268cf", 
             "workflow_outputs": [
@@ -484,22 +484,22 @@
                 }
             }, 
             "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\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"method\": \"\\\"k_option\\\"\"}", 
-            "tool_version": "1.1.2", 
+            "tool_version": "1.1.2.1", 
             "type": "tool", 
             "uuid": "749b801a-afe6-4a36-b13a-30de5d736a92", 
             "workflow_outputs": []
         }, 
         "10": {
             "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": 10, 
             "input_connections": {
                 "input": {
@@ -553,22 +553,22 @@
                 }
             }, 
             "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\\\": \\\"history\\\", \\\"ownFile\\\": null, \\\"__current_case__\\\": 1}\", \"method\": \"\\\"k_option\\\"\"}", 
-            "tool_version": "1.1.2", 
+            "tool_version": "1.1.2.1", 
             "type": "tool", 
             "uuid": "ff1dd365-8697-42f6-bad7-81ee0ec61e3e", 
             "workflow_outputs": []
         }, 
         "11": {
             "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": 11, 
             "input_connections": {
                 "inputs_0|input": {
@@ -599,15 +599,15 @@
                 }
             }, 
             "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": "a9ea9af5-d524-4f62-8969-70cbc5be79dd", 
             "workflow_outputs": [
@@ -620,7 +620,7 @@
         }, 
         "12": {
             "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.06", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_wrapper/0.1.08", 
             "id": 12, 
             "input_connections": {
                 "db_opts|histdb": {
@@ -647,15 +647,15 @@
             }, 
             "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_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastx_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\\\"\", \"__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", 
+            "tool_version": "0.1.08", 
             "type": "tool", 
             "uuid": "b9891d9f-e295-4ffd-aa8e-a8c8f76efe59", 
             "workflow_outputs": [
@@ -997,7 +997,7 @@
         }, 
         "18": {
             "annotation": "", 
-            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.1.06", 
+            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_wrapper/0.1.08", 
             "id": 18, 
             "input_connections": {
                 "db_opts|histdb": {
@@ -1024,15 +1024,15 @@
             }, 
             "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_id": "toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_tblastx_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\\\"\", \"__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", 
+            "tool_version": "0.1.08", 
             "type": "tool", 
             "uuid": "43f3188c-43ca-41a0-9918-38fc03977321", 
             "workflow_outputs": [