# HG changeset patch
# User peterjc
# Date 1377104511 14400
# Node ID 3c280e01b9202ffc59c40ecd5429641affe4e162
# Parent 1a1ab2f2b5b548959ffe068cbb1b45de46ebf11b
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 1a1ab2f2b5b5 -r 3c280e01b920 README.rst
--- a/README.rst Mon Aug 19 11:35:52 2013 -0400
+++ b/README.rst Wed Aug 21 13:01:51 2013 -0400
@@ -5,6 +5,30 @@
See http://www.galaxyproject.org for information about the Galaxy Project.
+Sample Data
+===========
+
+This workflow was developed and run on several Phytophthora species.
+For example, try the "Phyca11" protein set for Phytophthora capsici:
+
+http://genome.jgi-psf.org/Phyca11/download/Phyca11_filtered_proteins.fasta.gz
+
+You can upload this directly into Galaxy via this URL. Galaxy will handle
+removing the gzip compression to give you the FASTA protein file which
+has 19,805 protein sequences. The expected results:
+
+* 89 RXLRs using Whisson et al. (2007)
+* 124 RXLRs using Win et al. (2007)
+* 162 RXLRs using Bhattacharjee et al. (2006)
+
+Of these, only 79 sequences pass all three of the RXLR prediction tools,
+while 19643 have no RXLR matches at all.
+
+.. image:: https://raw.github.com/peterjc/picobio/master/galaxy_workflows/rxlr_venn_workflow/Phyca11_example_output.png
+ :height: 400px
+ :width: 400px
+
+
Citation
========
@@ -63,6 +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 1a1ab2f2b5b5 -r 3c280e01b920 rxlr_venn_workflow.ga
--- a/rxlr_venn_workflow.ga Mon Aug 19 11:35:52 2013 -0400
+++ b/rxlr_venn_workflow.ga Wed Aug 21 13:01:51 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": []