Mercurial > repos > peterjc > rxlr_venn_workflow

changeset 4:3c280e01b920 draft

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Uploaded v0.0.2, bump tool version numbers to fix warning about Filter1 parameter, adding link to Tool Shed in annotation. No functional changes.
author peterjc
date Wed, 21 Aug 2013 13:01:51 -0400
parents 1a1ab2f2b5b5
children 4726b640f221
files README.rst rxlr_venn_workflow.ga
diffstat 2 files changed, 53 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- 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
 ==========
 
--- 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.<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).", 
     "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": []