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changeset 3:b0b927299aee draft

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Uploaded v0.0.11 with automatic dependency installation. The Python wrapper also gives specific errors for partial installation issues.
author peterjc
date Thu, 16 May 2013 04:45:41 -0400
parents 5a8e09f115f8
children f7ce32e13bc6
files tools/effectiveT3/effectiveT3.py tools/effectiveT3/effectiveT3.txt tools/effectiveT3/effectiveT3.xml tools/effectiveT3/tool_dependencies.xml tools/protein_analysis/effectiveT3.py tools/protein_analysis/effectiveT3.txt tools/protein_analysis/effectiveT3.xml
diffstat 7 files changed, 404 insertions(+), 341 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/effectiveT3/effectiveT3.py	Thu May 16 04:45:41 2013 -0400
@@ -0,0 +1,151 @@
+#!/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
+
+#The Galaxy auto-install via tool_dependencies.xml will set this environment variable
+effectiveT3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
+effectiveT3_jar = os.path.join(effectiveT3_dir, "TTSS_GUI-1.0.1.jar")
+
+if "-v" in sys.argv or "--version" in sys.argv:
+    #TODO - Get version of the JAR file dynamically?
+    print "Wrapper v0.0.11, TTSS_GUI-1.0.1.jar"
+    sys.exit(0)
+
+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.isdir(effectiveT3_dir):
+    stop_err("Effective T3 folder not found: %r" % effectiveT3_dir)
+
+if not os.path.isfile(effectiveT3_jar):
+    stop_err("Effective T3 JAR file not found: %r" % effectiveT3_jar)
+
+if not os.path.isdir(os.path.join(effectiveT3_dir, "module")):
+    stop_err("Effective T3 module folder not found: %r" % os.path.join(effectiveT3_dir, "module"))
+
+effectiveT3_model = os.path.join(effectiveT3_dir, "module", model)
+if not os.path.isfile(effectiveT3_model):
+    sys.stderr.write("Contents of %r is %s\n"
+                     % (os.path.join(effectiveT3_dir, "module"),
+                        ", ".join(repr(p) for p in os.listdir(os.path.join(effectiveT3_dir, "module")))))
+    sys.stderr.write("Main JAR was found: %r\n" % effectiveT3_jar)
+    stop_err("Effective T3 model JAR file not found: %r" % 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")
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/effectiveT3/effectiveT3.txt	Thu May 16 04:45:41 2013 -0400
@@ -0,0 +1,129 @@
+Galaxy wrapper for EffectiveT3 v1.0.1
+=====================================
+
+This wrapper is copyright 2011-2013 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/
+
+This wrapper is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and install
+the Jar files for effectiveT3 v1.0.1 and the three models (animal, plant and std).
+
+
+Manual Installation
+===================
+
+You can change the path by setting the environment variable EFFECTIVET3 to the
+relevant folder, 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/effectiveT3 folder:
+
+* effectiveT3.xml (the Galaxy tool definition)
+* effectiveT3.py (the Python wrapper script)
+* effectiveT3.txt (this README file)
+
+Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder
+(and edit if appropriate, e.g. to add or remove a model).
+
+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="effectiveT3/effectiveT3.xml" />
+
+If you wish to run the unit tests, also add this to tools_conf.xml.sample
+and move/copy the test-data files under Galaxy's test-data folder.
+
+$ ./run_functional_tests.sh -id effectiveT3
+
+That's it.
+
+
+History
+=======
+
+v0.0.7 - Initial public release
+v0.0.8 - Include effectiveT3.loc.sample in Tool Shed
+v0.0.9 - Check the return code for errors in the XML
+v0.0.10- Added unit test
+v0.0.11- Automated installation
+       - Record version of Python script when called from Galaxy
+       - Link to Tool Shed added to help text and this documentation.
+
+
+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://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder:
+
+$ tar -czf effectiveT3.tar.gz tools/effectiveT3/effectiveT3.xml tools/effectiveT3/effectiveT3.py tools/effectiveT3/effectiveT3.txt tools/effectiveT3/tool_dependencies.xml tool-data/effectiveT3.loc.sample test-data/four_human_proteins.fasta test-data/four_human_proteins.effectiveT3.tabular test-data/empty.fasta test-data/empty_effectiveT3.tabular
+
+
+Check this worked:
+
+$ tar -tzf effectiveT3.tar.gz
+tools/effectiveT3/effectiveT3.xml
+tools/effectiveT3/effectiveT3.py
+tools/effectiveT3/effectiveT3.txt
+tools/effectiveT3/tool_dependencies.xml
+tool-data/effectiveT3.loc.sample
+test-data/four_human_proteins.fasta
+test-data/four_human_proteins.effectiveT3.tabular
+test-data/empty.fasta
+test-data/empty_effectiveT3.tabular
+
+
+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.
+EffectiveT3 is available and licenced separately.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/effectiveT3/effectiveT3.xml	Thu May 16 04:45:41 2013 -0400
@@ -0,0 +1,94 @@
+<tool id="effectiveT3" name="Effective T3" version="0.0.11">
+    <description>Find bacterial effectors in protein sequences</description>
+    <requirements>
+        <requirement type="package" version="1.0.1">effectiveT3</requirement>
+    </requirements>
+    <version_command interpreter="python">effectiveT3.py --version</version_command>
+    <command interpreter="python">
+effectiveT3.py $module.fields.path
+#if $restrict.type=="cutoff":
+  cutoff=$restrict.cutoff
+#else:
+  $restrict.type
+#end if
+$fasta_file $tabular_file</command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+    <inputs>
+        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
+        <param name="module" type="select" display="radio" label="Classification module">
+            <options from_file="effectiveT3.loc">
+                <column name="value" index="0"/>
+                <column name="name" index="1"/>
+                <column name="path" index="2"/>
+            </options>
+        </param>
+        <conditional name="restrict">
+            <param name="type" type="select" label="Cut-off setting">
+                <option value="selective">Selective (threshold set in module)</option>
+                <option value="sensitive">Sensitive (threshold set in module)</option>
+                <option value="cutoff">User defined cut-off</option>
+            </param>
+            <when value="selective" />
+            <when value="sensitive" />
+            <when value="cutoff" >
+                <param name="cutoff" type="float" min="0" max="1" label="Cut-off" value="" help="Threshold cut-off between 0 and 1"  />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="tabular_file" format="tabular" label="$module.value_label results" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
+            <param name="module" value="animal" />
+            <param name="type" value="selective" />
+            <output name="tabular_file" file="four_human_proteins.effectiveT3.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="fasta_file" value="empty.fasta" ftype="fasta" />
+            <param name="module" value="plant" />
+            <param name="type" value="sensistive" />
+            <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" />
+        </test>
+    </tests>
+    <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):
+
+====== ==============================================================================
+Column Description
+------ ------------------------------------------------------------------------------
+     1 Sequence identifier
+     2 Sequence description (from the FASTA file)
+     3 Score (between 0 and 1, or negative for an error such as a very short peptide)
+     4 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/
+
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
+    </help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/effectiveT3/tool_dependencies.xml	Thu May 16 04:45:41 2013 -0400
@@ -0,0 +1,30 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="effectiveT3" version="1.0.1">
+        <install version="1.0">
+            <actions>
+                <!-- Set environment variable so Python script knows where to look -->
+                <action type="set_environment">
+                    <environment_variable name="EFFECTIVET3" action="set_to">$INSTALL_DIR</environment_variable>
+                </action>
+                <!-- Main JAR file -->
+                <action type="shell_command">wget http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action>
+		<!-- If using action type download_file will need to move the file,
+                <action type="move_file"><source>TTSS_GUI-1.0.1.jar</source><destination>$INSTALL_DIR/</destination></action>
+		-->
+                <!-- Three model JAR files -->
+                <action type="make_directory">$INSTALL_DIR/module</action>
+                <action type="shell_command">wget http://effectors.org/download/module/TTSS_ANIMAL-1.0.1.jar</action>
+                <action type="move_file"><source>TTSS_ANIMAL-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>		
+                <action type="shell_command">wget http://effectors.org/download/module/TTSS_PLANT-1.0.1.jar</action>
+                <action type="move_file"><source>TTSS_PLANT-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>
+                <action type="shell_command">wget http://effectors.org/download/module/TTSS_STD-1.0.1.jar</action>
+                <action type="move_file"><source>TTSS_STD-1.0.1.jar</source><destination>$INSTALL_DIR/module/</destination></action>
+            </actions>
+        </install>
+        <readme>
+Downloads effectiveT3 v1.0.1 and the three models from http://effectors.org/
+        </readme>
+    </package>
+</tool_dependency>
+
--- a/tools/protein_analysis/effectiveT3.py	Wed Apr 17 05:26:26 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,140 +0,0 @@
-#!/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")
--- a/tools/protein_analysis/effectiveT3.txt	Wed Apr 17 05:26:26 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,113 +0,0 @@
-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/
-
-
-Installation
-============
-
-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)
-
-Also copy effectiveT3.loc.sample to effectiveT3.loc in the tool-data folder
-(and edit if appropriate, e.g. to add or remove a model).
-
-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" />
-
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder.
-
-That's it.
-
-
-History
-=======
-
-v0.0.7 - Initial public release
-v0.0.8 - Include effectiveT3.loc.sample in Tool Shed
-v0.0.9 - Check the return code for errors in the XML
-v0.0.10- Added unit test
-
-
-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://toolshed.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 tool-data/effectiveT3.loc.sample test-data/four_human_proteins.fasta test-data/four_human_proteins.effectiveT3.tabular test-data/empty.fasta test-data/empty_effectiveT3.tabular
-
-
-Check this worked:
-
-$ tar -tzf effectiveT3.tar.gz
-tools/protein_analysis/effectiveT3.xml
-tools/protein_analysis/effectiveT3.py
-tools/protein_analysis/effectiveT3.txt
-tool-data/effectiveT3.loc.sample
-test-data/four_human_proteins.fasta
-test-data/four_human_proteins.effectiveT3.tabular
-test-data/empty.fasta
-test-data/empty_effectiveT3.tabular
-
-
-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.
-EffectiveT3 is available and licenced separately.
--- a/tools/protein_analysis/effectiveT3.xml	Wed Apr 17 05:26:26 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-<tool id="effectiveT3" name="Effective T3" version="0.0.10">
-    <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 $tabular_file</command>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-    </stdio>
-    <inputs>
-        <param name="fasta_file" type="data" format="fasta" label="FASTA file of protein sequences"/> 
-        <param name="module" type="select" display="radio" label="Classification module">
-            <options from_file="effectiveT3.loc">
-                <column name="value" index="0"/>
-                <column name="name" index="1"/>
-                <column name="path" index="2"/>
-            </options>
-        </param>
-        <conditional name="restrict">
-            <param name="type" type="select" label="Cut-off setting">
-                <option value="selective">Selective (threshold set in module)</option>
-                <option value="sensitive">Sensitive (threshold set in module)</option>
-                <option value="cutoff">User defined cut-off</option>
-            </param>
-            <when value="selective" />
-            <when value="sensitive" />
-            <when value="cutoff" >
-                <param name="cutoff" type="float" min="0" max="1" label="Cut-off" value="" help="Threshold cut-off between 0 and 1"  />
-            </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="tabular_file" format="tabular" label="$module.value_label results" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="fasta_file" value="four_human_proteins.fasta" ftype="fasta" />
-            <param name="module" value="animal" />
-            <param name="type" value="selective" />
-            <output name="tabular_file" file="four_human_proteins.effectiveT3.tabular" ftype="tabular" />
-        </test>
-        <test>
-            <param name="fasta_file" value="empty.fasta" ftype="fasta" />
-            <param name="module" value="plant" />
-            <param name="type" value="sensistive" />
-            <output name="tabular_file" file="empty_effectiveT3.tabular" ftype="tabular" />
-        </test>
-    </tests>
-    <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):
-
-====== ==============================================================================
-Column Description
------- ------------------------------------------------------------------------------
-     1 Sequence identifier
-     2 Sequence description (from the FASTA file)
-     3 Score (between 0 and 1, or negative for an error such as a very short peptide)
-     4 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>