# HG changeset patch
# User peterjc
# Date 1369327758 14400
# Node ID 4cd848c5590b4ac22542355993721cc9322bef75
# Parent  2b35b5c4b7f49da0b5628ee5fe01b6da624ae19c
Uploaded v0.2.5 preview 3, use $NSLOTS in the PSORT wrappers.

diff -r 2b35b5c4b7f4 -r 4cd848c5590b tools/protein_analysis/promoter2.xml
--- a/tools/protein_analysis/promoter2.xml	Fri May 10 07:48:26 2013 -0400
+++ b/tools/protein_analysis/promoter2.xml	Thu May 23 12:49:18 2013 -0400
@@ -1,13 +1,15 @@
-<tool id="promoter2" name="Promoter 2.0" version="0.0.5">
+<tool id="promoter2" name="Promoter 2.0" version="0.0.6">
     <description>Find eukaryotic PolII promoters in DNA sequences</description>
     <!-- If job splitting is enabled, break up the query file into parts -->
     <!-- Using 2000 per chunk so 4 threads each doing 500 is ideal -->
     <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
     <command interpreter="python">
         promoter2.py "\$NSLOTS" $fasta_file $tabular_file
+        ##I want the number of threads to be a Galaxy config option...
         ##Set the number of threads in the runner entry in universe_wsgi.ini
         ##which (on SGE at least) will set the $NSLOTS environment variable.
-        ##If the environment variable isn't set, get "", and defaults to one.
+        ##If the environment variable isn't set, get "", and the python wrapper
+        ##defaults to four threads.
     </command>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -41,10 +43,14 @@
 
 The input is a FASTA file of nucleotide sequences (e.g. upstream regions of your genes), and the output is tabular with five columns (one row per promoter):
 
- 1. Sequence identifier (first word of FASTA header)
- 2. Promoter position, e.g. 600
- 3. Promoter score, e.g. 1.063
- 4. Promoter likelihood, e.g. Highly likely prediction
+====== ==================================================
+Column Description
+------ --------------------------------------------------
+     1 Sequence identifier (first word of FASTA header)
+     2 Promoter position, e.g. 600
+     3 Promoter score, e.g. 1.063
+     4 Promoter likelihood, e.g. Highly likely prediction
+====== ==================================================
 
 The scores are classified very simply as follows:
 
diff -r 2b35b5c4b7f4 -r 4cd848c5590b tools/protein_analysis/psortb.xml
--- a/tools/protein_analysis/psortb.xml	Fri May 10 07:48:26 2013 -0400
+++ b/tools/protein_analysis/psortb.xml	Thu May 23 12:49:18 2013 -0400
@@ -1,10 +1,17 @@
-<tool id="Psortb" name="psortb" version="0.0.2">
+<tool id="Psortb" name="psortb" version="0.0.3">
   <description>Determines sub-cellular localisation of bacterial/archaeal protein sequences</description>
   <!-- If job splitting is enabled, break up the query file into parts -->
   <!-- Using 2000 chunks meaning 4 threads doing 500 each is ideal -->
   <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
   <version_command interpreter="python">psortb.py --version</version_command>
-  <command interpreter="python">psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"</command>
+  <command interpreter="python">
+    psortb.py "\$NSLOTS" "$type" "$long" "$cutoff" "$divergent" "$sequence" "$outfile"
+    ##I want the number of threads to be a Galaxy config option...
+    ##Set the number of threads in the runner entry in universe_wsgi.ini
+    ##which (on SGE at least) will set the $NSLOTS environment variable.
+    ##If the environment variable isn't set, get "", and python wrapper
+    ##defaults to four threads.
+  </command>
   <stdio>
     <!-- Anything other than zero is an error -->
     <exit_code range="1:" />
diff -r 2b35b5c4b7f4 -r 4cd848c5590b tools/protein_analysis/signalp3.xml
--- a/tools/protein_analysis/signalp3.xml	Fri May 10 07:48:26 2013 -0400
+++ b/tools/protein_analysis/signalp3.xml	Thu May 23 12:49:18 2013 -0400
@@ -7,7 +7,8 @@
       signalp3.py $organism $truncate "\$NSLOTS" $fasta_file $tabular_file
       ##Set the number of threads in the runner entry in universe_wsgi.ini
       ##which (on SGE at least) will set the $NSLOTS environment variable.
-      ##If the environment variable isn't set, get "", and defaults to one.
+      ##If the environment variable isn't set, get "", and the python wrapper
+      ##defaults to four threads.
     </command>
     <stdio>
         <!-- Anything other than zero is an error -->
diff -r 2b35b5c4b7f4 -r 4cd848c5590b tools/protein_analysis/tmhmm2.xml
--- a/tools/protein_analysis/tmhmm2.xml	Fri May 10 07:48:26 2013 -0400
+++ b/tools/protein_analysis/tmhmm2.xml	Thu May 23 12:49:18 2013 -0400
@@ -5,9 +5,11 @@
     <parallelism method="basic" split_inputs="fasta_file" split_mode="to_size" split_size="2000" merge_outputs="tabular_file"></parallelism>
     <command interpreter="python">
       tmhmm2.py "\$NSLOTS" $fasta_file $tabular_file
+      ##I want the number of threads to be a Galaxy config option...
       ##Set the number of threads in the runner entry in universe_wsgi.ini
       ##which (on SGE at least) will set the $NSLOTS environment variable.
-      ##If the environment variable isn't set, get "", and defaults to one.
+      ##If the environment variable isn't set, get "", and the python wrapper
+      ##defaults to four threads.
     </command>
     <stdio>
         <!-- Anything other than zero is an error -->
diff -r 2b35b5c4b7f4 -r 4cd848c5590b tools/protein_analysis/wolf_psort.xml
--- a/tools/protein_analysis/wolf_psort.xml	Fri May 10 07:48:26 2013 -0400
+++ b/tools/protein_analysis/wolf_psort.xml	Thu May 23 12:49:18 2013 -0400
@@ -1,8 +1,12 @@
-<tool id="wolf_psort" name="WoLF PSORT" version="0.0.5">
+<tool id="wolf_psort" name="WoLF PSORT" version="0.0.6">
     <description>Eukaryote protein subcellular localization prediction</description>
     <command interpreter="python">
-      wolf_psort.py $organism 8 $fasta_file $tabular_file
+      wolf_psort.py $organism "\$NSLOTS" "$fasta_file" "$tabular_file"
       ##I want the number of threads to be a Galaxy config option...
+      ##Set the number of threads in the runner entry in universe_wsgi.ini
+      ##which (on SGE at least) will set the $NSLOTS environment variable.
+      ##If the environment variable isn't set, get "", and python wrapper
+      ##defaults to four threads.
     </command>
     <stdio>
         <!-- Anything other than zero is an error -->
@@ -84,6 +88,11 @@
 vacu   vacuolar membrane     0005774(2)
 ====== ===================== =====================
 
+Numbers in parentheses, such as "0005856(2)" indicate that descendant "part_of"
+cellular components were also included, up to the specified depth (2 in this case).
+For example, all of the children and grandchildren of "GO:0005856" were
+included as "cysk". 
+
 Additionally compound predictions like mito_nucl are also given.