Mercurial > repos > peterjc > secreted_protein_workflow

changeset 2:3a0c0d1c388f draft

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Uploaded v0.0.2, updated tool versions to solve warning from core Galaxy filter tool being updated. No functional changes.
author peterjc
date Wed, 21 Aug 2013 11:58:54 -0400
parents 606da4e1d925
children 72f03c2102ee
files README.rst secreted_protein_workflow.ga
diffstat 2 files changed, 39 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Mon Aug 19 11:37:04 2013 -0400
+++ b/README.rst	Wed Aug 21 11:58:54 2013 -0400
@@ -4,12 +4,26 @@
 It runs SignalP v3.0 (Bendtsen et al. 2004) and selects only proteins with a
 strong predicted signal peptide, and then runs TMHMM v2.0 (Krogh et al. 2001)
 on those, and selects only proteins without a predicted trans-membrane helix.
-This workflow was used in Kikuchi et al (2001), and is a simplification of
-the candidate effector protocol described in Jones et al (2009).
+This workflow was used in Kikuchi et al. (2011), and is a simplification of
+the candidate effector protocol described in Jones et al. (2009).
 
 See http://www.galaxyproject.org for information about the Galaxy Project.
 
 
+Sample Data
+===========
+
+This workflow was developed and run on several nematode species. For example,
+try the protein set for Bursaphelenchus xylophilus (Kikuchi et al. 2011):
+
+ftp://ftp.sanger.ac.uk/pub/pathogens/Bursaphelenchus/xylophilus/Assembly-v1.2/BUX.v1.2.genedb.protein.fa.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
+18,074 sequences. The expected result (selecting organism type Eukaryote)
+is a FASTA protein file of 2,297 predicted secreted protein sequences.
+
+
 Citation
 ========
 
@@ -78,6 +92,19 @@
 installation (SignalP v3.0 and TMHMM v2.0).
 
 
+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.
+======= ======================================================================
+
+
 Developers
 ==========
 
--- a/secreted_protein_workflow.ga	Mon Aug 19 11:37:04 2013 -0400
+++ b/secreted_protein_workflow.ga	Wed Aug 21 11:58:54 2013 -0400
@@ -62,8 +62,8 @@
             }, 
             "tool_errors": null, 
             "tool_id": "signalp3", 
-            "tool_state": "{\"organism\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"truncate\": \"\\\"60\\\"\", \"__page__\": 0}", 
-            "tool_version": "0.0.8", 
+            "tool_state": "{\"__page__\": 0, \"truncate\": \"\\\"60\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"fasta_file\": \"null\", \"organism\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"__rerun_remap_job_id__\": null}", 
+            "tool_version": "0.0.12", 
             "type": "tool", 
             "user_outputs": []
         }, 
@@ -104,7 +104,7 @@
             }, 
             "tool_errors": null, 
             "tool_id": "Filter1", 
-            "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c14=='Y' or c15=='S'\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c14=='Y' or c15=='S'\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
             "tool_version": "1.1.0", 
             "type": "tool", 
             "user_outputs": []
@@ -152,8 +152,8 @@
             }, 
             "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_version": "0.0.1", 
+            "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": []
         }, 
@@ -187,8 +187,8 @@
             }, 
             "tool_errors": null, 
             "tool_id": "tmhmm2", 
-            "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
-            "tool_version": "0.0.7", 
+            "tool_state": "{\"__page__\": 0, \"fasta_file\": \"null\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}", 
+            "tool_version": "0.0.11", 
             "type": "tool", 
             "user_outputs": []
         }, 
@@ -229,7 +229,7 @@
             }, 
             "tool_errors": null, 
             "tool_id": "Filter1", 
-            "tool_state": "{\"__page__\": 0, \"cond\": \"\\\"c5== 0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\", \"input\": \"null\"}", 
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"cond\": \"\\\"c5== 0\\\"\", \"input\": \"null\", \"header_lines\": \"\\\"0\\\"\", \"chromInfo\": \"\\\"/opt/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\"\"}", 
             "tool_version": "1.1.0", 
             "type": "tool", 
             "user_outputs": []
@@ -279,8 +279,8 @@
             }, 
             "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_version": "0.0.1", 
+            "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": []
         }