Mercurial > repos > drosofff > metavisitor_workflows

diff Galaxy-Workflow-Metavisitor__Workflow_for_Use_Case_3-1.ga @ 2:48b020a0d2f7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/workflows commit d5feabb3309f2da09ba15b5fe818d0a7b30f3266
author drosofff
date Fri, 13 May 2016 05:46:40 -0400
parents 4a47903bb4df
children ba15c770fd40
line wrap: on
line diff
--- 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": 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": "f73e38bc-8998-4e77-9d4e-77c8748f3a71", 
@@ -290,6 +314,12 @@
             }, 
             "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\\\": \\\"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\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"vir1\\\", \\\"__current_case__\\\": 0}\", \"method\": \"\\\"k_option\\\"\"}", 
             "tool_version": "1.1.2", 
             "type": "tool", 
@@ -391,6 +427,12 @@
             }, 
             "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\": \"\\\"27\\\"\", \"__rerun_remap_job_id__\": null, \"start_hash_length\": \"\\\"11\\\"\"}", 
             "tool_version": "1.1.4", 
             "type": "tool", 
@@ -441,6 +483,12 @@
             }, 
             "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", 
@@ -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",