# HG changeset patch
# User peterjc
# Date 1377104443 14400
# Node ID 923fa257756453ba2547e57bb68304158f0738d4
# Parent de29af5da85ead13e84121d3353d43c702235224
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
diff -r de29af5da85e -r 923fa2577564 README.rst
--- a/README.rst Tue Aug 20 06:53:57 2013 -0400
+++ b/README.rst Wed Aug 21 13:00:43 2013 -0400
@@ -87,6 +87,21 @@
HMMER v2.0, and the R/Bioconductor package limma).
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1 - Initial release to Tool Shed (May, 2013)
+ - Expanded README file to include example data
+v0.0.2 - Updated versions of the tools used, inclulding core Galaxy Filter
+ tool to avoid warning about new ``header_lines`` parameter.
+ - Added link to Tool Shed in the workflow annotation explaining there
+ is a README file with sample data, and a requested citation.
+======= ======================================================================
+
+
Developers
==========
diff -r de29af5da85e -r 923fa2577564 rxlr_venn_workflow.ga
--- a/rxlr_venn_workflow.ga Tue Aug 20 06:53:57 2013 -0400
+++ b/rxlr_venn_workflow.ga Wed Aug 21 13:00:43 2013 -0400
@@ -1,6 +1,6 @@
{
"a_galaxy_workflow": "true",
- "annotation": "",
+ "annotation": "Takes a protein FASTA file, runs three different RXLR motif methods, draws a Venn diagram comparing them, and creates a FASTA file of those proteins passing all three screens.
\n
\nThis workflow is available on the Galaxy Tool Shed with a README file giving more information including sample data, and full citation details (Cock and Pritchard 2013).",
"format-version": "0.1",
"name": "3 RXLR methods, Venn Diagram, overlap FASTA",
"steps": {
@@ -57,8 +57,8 @@
},
"tool_errors": null,
"tool_id": "rxlr_motifs",
- "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Whisson2007\\\"\"}",
- "tool_version": "0.0.6",
+ "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Whisson2007\\\"\"}",
+ "tool_version": "0.0.7",
"type": "tool",
"user_outputs": []
},
@@ -92,8 +92,8 @@
},
"tool_errors": null,
"tool_id": "rxlr_motifs",
- "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Win2007\\\"\"}",
- "tool_version": "0.0.6",
+ "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Win2007\\\"\"}",
+ "tool_version": "0.0.7",
"type": "tool",
"user_outputs": []
},
@@ -127,8 +127,8 @@
},
"tool_errors": null,
"tool_id": "rxlr_motifs",
- "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Bhattacharjee2006\\\"\"}",
- "tool_version": "0.0.6",
+ "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"model\": \"\\\"Bhattacharjee2006\\\"\"}",
+ "tool_version": "0.0.7",
"type": "tool",
"user_outputs": []
},
@@ -169,7 +169,7 @@
},
"tool_errors": null,
"tool_id": "Filter1",
- "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c2=='Y'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}",
+ "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2=='Y'\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"tool_version": "1.1.0",
"type": "tool",
"user_outputs": []
@@ -211,7 +211,7 @@
},
"tool_errors": null,
"tool_id": "Filter1",
- "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c2=='Y'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}",
+ "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2=='Y'\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"tool_version": "1.1.0",
"type": "tool",
"user_outputs": []
@@ -253,7 +253,7 @@
},
"tool_errors": null,
"tool_id": "Filter1",
- "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c2=='Y'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}",
+ "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c2=='Y'\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"tool_version": "1.1.0",
"type": "tool",
"user_outputs": []
@@ -308,7 +308,7 @@
},
"tool_errors": null,
"tool_id": "seq_filter_by_id",
- "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}",
+ "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}",
"tool_version": "0.0.5",
"type": "tool",
"user_outputs": []
@@ -357,7 +357,7 @@
},
"tool_errors": null,
"tool_id": "venn_list",
- "tool_state": "{\"__page__\": 0, \"universe\": \"{\\\"main\\\": null, \\\"type_select\\\": \\\"explicit\\\", \\\"__current_case__\\\": 0}\", \"sets\": \"[{\\\"__index__\\\": 0, \\\"set\\\": null, \\\"lab\\\": \\\"Whisson et al.\\\"}, {\\\"__index__\\\": 1, \\\"set\\\": null, \\\"lab\\\": \\\"Win et al.\\\"}, {\\\"__index__\\\": 2, \\\"set\\\": null, \\\"lab\\\": \\\"Bhattacharjee et al.\\\"}]\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"main_lab\": \"\\\"Venn Diagram comparing RXLR predictions\\\"\"}",
+ "tool_state": "{\"__page__\": 0, \"universe\": \"{\\\"main\\\": null, \\\"type_select\\\": \\\"explicit\\\", \\\"__current_case__\\\": 0}\", \"__rerun_remap_job_id__\": null, \"main_lab\": \"\\\"Venn Diagram comparing RXLR predictions\\\"\", \"sets\": \"[{\\\"__index__\\\": 0, \\\"set\\\": null, \\\"lab\\\": \\\"Whisson et al.\\\"}, {\\\"__index__\\\": 1, \\\"set\\\": null, \\\"lab\\\": \\\"Win et al.\\\"}, {\\\"__index__\\\": 2, \\\"set\\\": null, \\\"lab\\\": \\\"Bhattacharjee et al.\\\"}]\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}",
"tool_version": "0.0.4",
"type": "tool",
"user_outputs": []
@@ -412,7 +412,7 @@
},
"tool_errors": null,
"tool_id": "seq_filter_by_id",
- "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}",
+ "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}",
"tool_version": "0.0.5",
"type": "tool",
"user_outputs": []
@@ -462,7 +462,7 @@
},
"tool_errors": null,
"tool_id": "seq_filter_by_id",
- "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}",
+ "tool_state": "{\"__page__\": 0, \"output_choice_cond\": \"{\\\"output_choice\\\": \\\"pos\\\", \\\"__current_case__\\\": 1}\", \"input_file\": \"null\", \"__rerun_remap_job_id__\": null, \"input_tabular\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"columns\": \"{\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": [\\\"1\\\"]}\"}",
"tool_version": "0.0.5",
"type": "tool",
"user_outputs": []