# HG changeset patch
# User peterjc
# Date 1307481690 14400
# Node ID 43436379876f564d050cd1e42402d7be20e0fcfc

Migrated tool version 0.0.7 from old tool shed archive to new tool shed repository

diff -r 000000000000 -r 43436379876f tools/protein_analysis/effectiveT3.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/protein_analysis/effectiveT3.py	Tue Jun 07 17:21:30 2011 -0400
@@ -0,0 +1,140 @@
+#!/usr/bin/env python
+"""Wrapper for EffectiveT3 v1.0.1 for use in Galaxy.
+
+This script takes exactly five command line arguments:
+ * model name (e.g. TTSS_STD-1.0.1.jar)
+ * threshold (selective or sensitive)
+ * an input protein FASTA filename
+ * output tabular filename
+
+It then calls the standalone Effective T3 v1.0.1 program (not the
+webservice), and reformats the semi-colon separated output into
+tab separated output for use in Galaxy.
+"""
+import sys
+import os
+import subprocess
+
+#You may need to edit this to match your local setup,
+effectiveT3_jar = "/opt/EffectiveT3/TTSS_GUI-1.0.1.jar"
+
+
+def stop_err(msg, error_level=1):
+   """Print error message to stdout and quit with given error level."""
+   sys.stderr.write("%s\n" % msg)
+   sys.exit(error_level)
+
+if len(sys.argv) != 5:
+   stop_err("Require four arguments: model, threshold, input protein FASTA file & output tabular file")
+
+model, threshold, fasta_file, tabular_file = sys.argv[1:]
+
+if not os.path.isfile(fasta_file):
+   stop_err("Input FASTA file not found: %s" % fasta_file)
+
+if threshold not in ["selective", "sensitive"] \
+and not threshold.startswith("cutoff="):
+   stop_err("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold)
+
+def clean_tabular(raw_handle, out_handle):
+    """Clean up Effective T3 output to make it tabular."""
+    count = 0
+    positive = 0
+    errors = 0
+    for line in raw_handle:
+        if not line or line.startswith("#") \
+        or line.startswith("Id; Description; Score;"):
+            continue
+        assert line.count(";") >= 3, repr(line)
+        #Normally there will just be three semi-colons, however the
+        #original FASTA file's ID or description might have had
+        #semi-colons in it as well, hence the following hackery:
+        try:
+            id_descr, score, effective = line.rstrip("\r\n").rsplit(";",2)
+            #Cope when there was no FASTA description
+            if "; " not in id_descr and id_descr.endswith(";"):
+                id = id_descr[:-1]
+                descr = ""
+            else:
+                id, descr = id_descr.split("; ",1)
+        except ValueError:
+            stop_err("Problem parsing line:\n%s\n" % line)
+        parts = [s.strip() for s in [id, descr, score, effective]]
+        out_handle.write("\t".join(parts) + "\n")
+        count += 1
+        if float(score) < 0:
+           errors += 1
+        if effective.lower() == "true":
+           positive += 1
+    return count, positive, errors
+
+def run(cmd):
+    #Avoid using shell=True when we call subprocess to ensure if the Python
+    #script is killed, so too is the child process.
+    try:
+        child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+    except Exception, err:
+        stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
+    #Use .communicate as can get deadlocks with .wait(),
+    stdout, stderr = child.communicate()
+    return_code = child.returncode
+    if return_code:
+        if stderr and stdout:
+            stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, err, stdout, stderr))
+        else:
+            stop_err("Return code %i from command:\n%s\n%s" % (return_code, err, stderr))
+
+if not os.path.isfile(effectiveT3_jar):
+   stop_err("Effective T3 JAR file not found: %s" % effectiveT3_jar)
+
+effectiveT3_dir = os.path.dirname(effectiveT3_jar)
+if not os.path.isdir(effectiveT3_dir):
+   stop_err("Effective T3 folder not found: %s" % effectiveT3_dir)
+
+effectiveT3_model = os.path.join(effectiveT3_dir, "module", model)
+if not os.path.isfile(effectiveT3_model):
+   stop_err("Effective T3 model JAR file not found: %s" % effectiveT3_model)
+
+#We will have write access whereever the output should be,
+temp_file = os.path.abspath(tabular_file + ".tmp")
+
+#Use absolute paths since will change current directory...
+tabular_file = os.path.abspath(tabular_file)
+fasta_file = os.path.abspath(fasta_file)
+
+cmd = ["java", "-jar", effectiveT3_jar,
+       "-f", fasta_file,
+       "-m", model,
+       "-t", threshold,
+       "-o", temp_file,
+       "-q"]
+
+try:
+    #Must run from directory above the module subfolder:
+    os.chdir(effectiveT3_dir)
+except:
+    stop_err("Could not change to Effective T3 folder: %s" % effectiveT3_dir)
+
+run(cmd)
+
+if not os.path.isfile(temp_file):
+   stop_err("ERROR - No output file from Effective T3")
+
+out_handle = open(tabular_file, "w")
+out_handle.write("#ID\tDescription\tScore\tEffective\n")
+data_handle = open(temp_file)
+count, positive, errors = clean_tabular(data_handle, out_handle)
+data_handle.close()
+out_handle.close()
+
+os.remove(temp_file)
+
+if errors:
+   print "%i sequences, %i positive, %i errors" \
+         % (count, positive, errors)
+else:
+   print "%i/%i sequences positive" % (positive, count)
+
+if count and count==errors:
+   #Galaxy will still  allow them to see the output file
+   stop_err("All your sequences gave an error code")
diff -r 000000000000 -r 43436379876f tools/protein_analysis/effectiveT3.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/protein_analysis/effectiveT3.txt	Tue Jun 07 17:21:30 2011 -0400
@@ -0,0 +1,94 @@
+Galaxy wrapper for EffectiveT3 v1.0.1
+=====================================
+
+This wrapper is copyright 2011 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+This is a wrapper for the command line Java tool EffectiveT3, v1.0.1,
+
+Jehl, Arnold and Rattei.
+Effective - a database of predicted secreted bacterial proteins
+Nucleic Acids Research, 39(Database issue), D591-5, 2011.
+http://dx.doi.org/10.1093/nar/gkq1154
+
+Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei.
+Sequence-based prediction of type III secreted proteins.
+PLoS Pathog. 5(4):e1000376, 2009.
+http://dx.doi.org/10.1371/journal.ppat.1000376
+
+http://effectors.org/
+
+You can change the path by editing the definition near the start of the Python
+script effectiveT3.py, but by default it expects the following files to be
+installed at these locations:
+
+/opt/EffectiveT3/TTSS_GUI-1.0.1.jar
+/opt/EffectiveT3/module/TTSS_ANIMAL-1.0.1.jar
+/opt/EffectiveT3/module/TTSS_PLANT-1.0.1.jar
+/opt/EffectiveT3/module/TTSS_STD-1.0.1.jar
+
+To install the wrapper copy or move the following files under the Galaxy tools
+folder, e.g. in a tools/protein_analysis folder:
+
+* effectiveT3.xml (the Galaxy tool definition)
+* effectiveT3.py (the Python wrapper script)
+* effectiveT3.txt (this README file)
+
+You will also need to modify the tools_conf.xml file to tell Galaxy to offer the
+tool. If you are using other protein analysis tools like TMHMM or SignalP, put
+it next to them. Just add the line:
+
+<tool file="protein_analysis/effectiveT3.xml" />
+
+That's it.
+
+
+History
+=======
+
+v0.0.7 - Initial public release
+
+
+Developers
+==========
+
+This script and related tools are being developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder:
+
+$ tar -czf effectiveT3.tar.gz tools/protein_analysis/effectiveT3.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt
+
+Check this worked:
+
+$ tar -tzf effectiveT3.tar.gz
+tools/protein_analysis/effectiveT3.xml
+tools/protein_analysis/effectiveT3.py
+tools/protein_analysis/effectiveT3.txt
+
+
+Licence (MIT/BSD style)
+=======================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
+
+NOTE: This is the licence for the Galaxy Wrapper only. NLStradamus
+is available and licenced separately.
diff -r 000000000000 -r 43436379876f tools/protein_analysis/effectiveT3.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/protein_analysis/effectiveT3.xml	Tue Jun 07 17:21:30 2011 -0400
@@ -0,0 +1,64 @@
+<tool id="effectiveT3" name="Effective T3" version="0.0.7">
+    <description>Find bacterial effectors in protein sequences</description>
+    <command interpreter="python">
+effectiveT3.py $module.fields.path
+#if $restrict.type=="cutoff":
+  cutoff=$restrict.cutoff
+#else:
+  $restrict.type
+#end if
+$fasta_file $tabular_file</command>
+    <inputs>
+        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
+        <param name="module" type="select" display="radio" label="Classification module">
+            <options from_file="effectiveT3.loc">
+                <column name="value" index="0"/>
+                <column name="name" index="1"/>
+                <column name="path" index="2"/>
+            </options>
+        </param>
+        <conditional name="restrict">
+            <param name="type" type="select" label="Cut-off setting">
+                <option value="selective">Selective (threshold set in module)</option>
+                <option value="sensitive">Sensitive (threshold set in module)</option>
+                <option value="cutoff">User defined cut-off</option>
+            </param>
+            <when value="selective" />
+            <when value="sensitive" />
+            <when value="cutoff" >
+                <param name="cutoff" type="float" min="0" max="1" label="Cut-off" value="" help="Threshold cut-off between 0 and 1"  />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="tabular_file" format="tabular" label="$module.value_label results" />
+    </outputs>
+    <help>
+    
+**What it does**
+
+This calls the command line Effective T3 v1.0.1 tool for prediction of bacterial effector proteins.
+
+The input is a FASTA file of protein sequences, and the output is tabular with four columns (one row per protein):
+
+ * Sequence identifier
+ * Sequence description (from the FASTA file)
+ * Score (between 0 and 1, or negative for an error such as a very short peptide)
+ * Predicted effector (true/false)
+
+**References**
+
+Jehl, Arnold and Rattei.
+Effective - a database of predicted secreted bacterial proteins
+Nucleic Acids Research, 39(Database issue), D591-5, 2011.
+http://dx.doi.org/10.1093/nar/gkq1154
+
+Arnold, Brandmaier, Kleine, Tischler, Heinz, Behrens, Niinikoski, Mewes, Horn and Rattei.
+Sequence-based prediction of type III secreted proteins.
+PLoS Pathog. 5(4):e1000376, 2009.
+http://dx.doi.org/10.1371/journal.ppat.1000376
+
+http://effectors.org/
+
+    </help>
+</tool>