Repository 'rxlr_venn_workflow'
hg clone https://toolshed.g2.bx.psu.edu/repos/peterjc/rxlr_venn_workflow

Changeset 4:3c280e01b920 (2013-08-21)
Previous changeset 3:1a1ab2f2b5b5 (2013-08-19) Next changeset 5:4726b640f221 (2013-10-25)
Commit message:
Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
modified:
README.rst
rxlr_venn_workflow.ga
b
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
b
@@ -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
 ==========
 
b
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
[
b'@@ -1,6 +1,6 @@\n {\n     "a_galaxy_workflow": "true", \n-    "annotation": "", \n+    "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.<br />\\n<br />\\nThis workflow is <a href=\\"http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow\\" target=\\"_blank\\">available on the Galaxy Tool Shed</a> with a README file giving more information including sample data, and full citation details (Cock and Pritchard 2013).", \n     "format-version": "0.1", \n     "name": "3 RXLR methods, Venn Diagram, overlap FASTA", \n     "steps": {\n@@ -57,8 +57,8 @@\n             }, \n             "tool_errors": null, \n             "tool_id": "rxlr_motifs", \n-            "tool_state": "{\\"__page__\\": 0, \\"fasta_file\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"model\\": \\"\\\\\\"Whisson2007\\\\\\"\\"}", \n-            "tool_version": "0.0.6", \n+            "tool_state": "{\\"__page__\\": 0, \\"fasta_file\\": \\"null\\", \\"__rerun_remap_job_id__\\": null, \\"chromInfo\\": \\"\\\\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"model\\": \\"\\\\\\"Whisson2007\\\\\\"\\"}", \n+            "tool_version": "0.0.7", \n             "type": "tool", \n             "user_outputs": []\n         }, \n@@ -92,8 +92,8 @@\n             }, \n             "tool_errors": null, \n             "tool_id": "rxlr_motifs", \n-            "tool_state": "{\\"__page__\\": 0, \\"fasta_file\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"model\\": \\"\\\\\\"Win2007\\\\\\"\\"}", \n-            "tool_version": "0.0.6", \n+            "tool_state": "{\\"__page__\\": 0, \\"fasta_file\\": \\"null\\", \\"__rerun_remap_job_id__\\": null, \\"chromInfo\\": \\"\\\\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"model\\": \\"\\\\\\"Win2007\\\\\\"\\"}", \n+            "tool_version": "0.0.7", \n             "type": "tool", \n             "user_outputs": []\n         }, \n@@ -127,8 +127,8 @@\n             }, \n             "tool_errors": null, \n             "tool_id": "rxlr_motifs", \n-            "tool_state": "{\\"__page__\\": 0, \\"fasta_file\\": \\"null\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"model\\": \\"\\\\\\"Bhattacharjee2006\\\\\\"\\"}", \n-            "tool_version": "0.0.6", \n+            "tool_state": "{\\"__page__\\": 0, \\"fasta_file\\": \\"null\\", \\"__rerun_remap_job_id__\\": null, \\"chromInfo\\": \\"\\\\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"model\\": \\"\\\\\\"Bhattacharjee2006\\\\\\"\\"}", \n+            "tool_version": "0.0.7", \n             "type": "tool", \n             "user_outputs": []\n         }, \n@@ -169,7 +169,7 @@\n             }, \n             "tool_errors": null, \n             "tool_id": "Filter1", \n-            "tool_state": "{\\"__page__\\": 0, \\"cond\\": \\"\\\\\\"c2==\'Y\'\\\\\\"\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"input\\": \\"null\\"}", \n+            "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\\\\\\"\\"}", \n             "tool_version": "1.1.0", \n             "type": "tool", \n             "user_outputs": []\n@@ -211,7 +211,7 @@\n             }, \n             "tool_errors": null, \n             "tool_id": "Filter1", \n-            "tool_state": "{\\"__page__\\": 0, \\"cond\\": \\"\\\\\\"c2==\'Y\'\\\\\\"\\", \\"chromInfo\\": \\"\\\\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"input\\": \\"null\\"}", \n+            "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\\\\\\"\\"}", \n             "tool_version": "1.1.0", \n             "type": "tool", \n             "user_outputs": []\n@@ -253,7 +253,7 @@\n    '..b'y-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"columns\\": \\"{\\\\\\"__class__\\\\\\": \\\\\\"UnvalidatedValue\\\\\\", \\\\\\"value\\\\\\": [\\\\\\"1\\\\\\"]}\\"}", \n+            "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\\\\\\"]}\\"}", \n             "tool_version": "0.0.5", \n             "type": "tool", \n             "user_outputs": []\n@@ -357,7 +357,7 @@\n             }, \n             "tool_errors": null, \n             "tool_id": "venn_list", \n-            "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\\\\\\"\\"}", \n+            "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\\\\\\"\\"}", \n             "tool_version": "0.0.4", \n             "type": "tool", \n             "user_outputs": []\n@@ -412,7 +412,7 @@\n             }, \n             "tool_errors": null, \n             "tool_id": "seq_filter_by_id", \n-            "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\\\\\\"]}\\"}", \n+            "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\\\\\\"]}\\"}", \n             "tool_version": "0.0.5", \n             "type": "tool", \n             "user_outputs": []\n@@ -462,7 +462,7 @@\n             }, \n             "tool_errors": null, \n             "tool_id": "seq_filter_by_id", \n-            "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\\\\\\"]}\\"}", \n+            "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\\\\\\"]}\\"}", \n             "tool_version": "0.0.5", \n             "type": "tool", \n             "user_outputs": []\n'