--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira3/README.rst	Thu Jan 30 13:21:21 2014 -0500
@@ -0,0 +1,125 @@
+Galaxy wrapper for the MIRA assembly program (v3.4)
+===================================================
+
+This tool 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 (MIT licence).
+
+This tool is a short Python script (to collect the MIRA output and move it
+to where Galaxy expects the files, and convert MIRA's TCS file into a tab
+separated file for use in Galaxy).
+
+It is available from the Galaxy Tool Shed at:
+http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and
+install the precompiled binary for MIRA v3.4.0 for the Galaxy wrapper,
+and run any tests.
+
+
+Manual Installation
+===================
+
+There are just two Galaxy files to install:
+
+* mira.py (the Python script)
+* mira.xml (the Galaxy tool definition)
+
+The suggested location is a new tools/mira3 folder. You will also need to
+modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
+this to tools_conf.xml.sample in order to run any tests::
+
+  <tool file="mira3/mira.xml" />
+
+You will also need to install MIRA, we used version 3.4.1.1. See:
+
+* http://chevreux.org/projects_mira.html
+* http://sourceforge.net/projects/mira-assembler/
+
+WARNING: This tool was initially developed to construct viral genome assembly
+and mapping pipelines, for which the run time and memory requirements are
+negligible. For larger tasks, be aware that MIRA can require vast amounts
+of RAM and run-times of over a week are possible. This tool wrapper makes
+no attempt to spot and reject such large jobs.
+
+
+History
+=======
+
+======= ======================================================================
+Version Changes
+------- ----------------------------------------------------------------------
+v0.0.1  - Initial version (working prototype, using MIRA 3.2.1)
+v0.0.2  - Improve capture of stdout/stderr (should see it as it runs)
+v0.0.3  - Support Ion Torrent reads, now requires MIRA 3.4.0 or later
+          (some other switches changed, e.g. -OUT rrol to rrot, which
+          means the wrapper no longer works with MIRA 3.2.x)
+        - The contig summary file (TCS file) was removed in MIRA 3.4
+        - Report all missing output files (not just first missing one)
+v0.0.4  - Fix problem with backbone arguments inroduced in v0.0.3
+v0.0.5  - Implement the <version_command> tag to record the wrapper
+          version and the MIRA version being used.
+        - Check using MIRA 3.4 (later versions have a different API)
+v0.0.6  - Tell MIRA to use /tmp for temporary files
+        - Tell MIRA to ignore long read names (otherwise it aborts)
+v0.0.7  - Automated installation of the 64 bit Linux MIRA binary.
+v0.0.8  - Basic unit test added (but commented out due to Galaxy issue).
+        - Link to Tool Shed added to help text and this documentation.
+        - Use reStructuredText for this README file.
+        - Adopted standard MIT licence.
+        - Updated citation information (Cock et al. 2013).
+        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
+v0.0.9  - Renamed folder mira_assembler to mira3 (see also MIRA 4 wrapper).
+        - Correct path issue in automated dependency installation
+======= ======================================================================
+
+
+Developers
+==========
+
+This script and related tools were initially developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+Development has now moved to a dedicated GitHub repository:
+https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder::
+
+    $ tar -czf mira3_wrapper.tar.gz tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/mira.py tools/mira3/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta
+
+Check this worked::
+
+    $ tar -tzf mira3_wrapper.tar.gz
+    tools/mira3/README.rst
+    tools/mira3/mira.xml
+    tools/mira3/mira.py
+    tools/mira3/tool_dependencies.xml
+    test-data/tvc_mini.fastq
+    test-data/tvc_contigs.fasta
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira3/mira.py	Thu Jan 30 13:21:21 2014 -0500
@@ -0,0 +1,125 @@
+#!/usr/bin/env python
+"""A simple wrapper script to call MIRA and collect its output.
+"""
+import os
+import sys
+import subprocess
+import shutil
+import time
+
+WRAPPER_VER = "0.0.5" #Keep in sync with the XML file
+
+def stop_err(msg, err=1):
+    sys.stderr.write(msg+"\n")
+    sys.exit(err)
+
+
+def get_version():
+    """Run MIRA to find its version number"""
+    # At the commend line I would use: mira -v | head -n 1
+    # however there is some pipe error when doing that here.
+    cmd = ["mira", "-v"]
+    try:
+        child = subprocess.Popen(cmd,
+                                 stdout=subprocess.PIPE,
+                                 stderr=subprocess.STDOUT)
+    except Exception, err:
+        sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
+        sys.exit(1)
+    ver, tmp = child.communicate()
+    del child
+    return ver.split("\n", 1)[0]
+
+
+mira_ver = get_version()
+if "V3.4." not in mira_ver:
+    stop_err("This wrapper is for MIRA V3.4, not %s" % mira_ver)
+if "-v" in sys.argv:
+    print "MIRA wrapper version %s," % WRAPPER_VER
+    print mira_ver
+    sys.exit(0)
+
+
+def collect_output(temp, name):
+    n3 = (temp, name, name, name)
+    f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
+    if not os.path.isdir(f):
+        stop_err("Missing output folder")
+    if not os.listdir(f):
+        stop_err("Empty output folder")
+    missing = []
+    for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
+                     ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
+                     ("%s/%s_out.wig" % (f, name), out_wig),
+                     ("%s/%s_out.caf" % (f, name), out_caf),
+                     ("%s/%s_out.ace" % (f, name), out_ace)]:
+        if not os.path.isfile(old):
+            missing.append(os.path.splitext(old)[-1])
+        else:
+            shutil.move(old, new)
+    if missing:
+        stop_err("Missing output files: %s" % ", ".join(missing))
+
+def clean_up(temp, name):
+    folder = "%s/%s_assembly" % (temp, name)
+    if os.path.isdir(folder):
+        shutil.rmtree(folder)
+
+#TODO - Run MIRA in /tmp or a configurable directory?
+#Currently Galaxy puts us somewhere safe like:
+#/opt/galaxy-dist/database/job_working_directory/846/
+temp = "."
+name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
+
+start_time = time.time()
+cmd_list =sys.argv[8:]
+cmd = " ".join(cmd_list)
+
+assert os.path.isdir(temp)
+d = "%s_assembly" % name
+assert not os.path.isdir(d), "Path %s already exists" % d
+try:
+    #Check path access
+    os.mkdir(d)
+except Exception, err:
+    sys.stderr.write("Error making directory %s\n%s" % (d, err))
+    sys.exit(1)
+
+#print os.path.abspath(".")
+#print cmd
+
+handle = open(out_log, "w")
+try:
+    #Run MIRA
+    child = subprocess.Popen(cmd_list,
+                             stdout=handle,
+                             stderr=subprocess.STDOUT)
+except Exception, err:
+    sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
+    #TODO - call clean up?
+    handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
+    handle.close()
+    sys.exit(1)
+#Use .communicate as can get deadlocks with .wait(),
+stdout, stderr = child.communicate()
+assert not stdout and not stderr #Should be empty as sent to handle
+run_time = time.time() - start_time
+return_code = child.returncode
+handle.write("\n\nMIRA took %0.2f minutes\n" % (run_time / 60.0))
+print "MIRA took %0.2f minutes" % (run_time / 60.0)
+if return_code:
+    handle.write("Return error code %i from command:\n" % return_code)
+    handle.write(cmd + "\n")
+    handle.close()
+    clean_up(temp, name)
+    stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
+             return_code)
+handle.close()
+
+#print "Collecting output..."
+collect_output(temp, name)
+
+#print "Cleaning up..."
+clean_up(temp, name)
+
+print "Done"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira3/mira.xml	Thu Jan 30 13:21:21 2014 -0500
@@ -0,0 +1,191 @@
+<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.8">
+    <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
+    <requirements>
+        <requirement type="binary">mira</requirement>
+        <requirement type="package" version="3.4.1.1">MIRA</requirement>
+    </requirements>
+    <version_command interpreter="python">mira.py -v</version_command>
+    <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
+##Give the wrapper script list of output filenames, then the mira command...
+mira --job=$job_method,$job_type,$job_quality
+
+##Input files
+#if $condBackbone.use == "true":
+    ## Can this be linked to job_method as well? If mapping we need the backbone...
+    -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
+#end if
+#if $condSanger.use == "true":
+    SANGER_SETTINGS
+    ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
+    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+    -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
+#end if
+#if $condRoche.use == "true":
+    454_SETTINGS
+    ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
+    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+    -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
+#end if
+#if $condIllumina.use == "true":
+    SOLEXA_SETTINGS
+    ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
+    -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
+    ##TODO - Look at -LR FASTQ qual offset (fqqo)
+#end if
+#if $condIonTorrent.use == "true":
+    IONTOR_SETTINGS
+    ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
+    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+    -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
+#end if
+
+##Output files
+COMMON_SETTINGS
+
+##ignore warnings about long read names
+-MI:somrnl=0
+
+##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
+##Explicitly disable formats we won't use like MAF (reduce IO)
+-OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
+
+##remove_rollover_tmps, remove_tmp_directory
+-OUT:rrot=1:rtd=1
+
+##put mira temp directory on local storage                                                                              
+-DI:trt=/tmp
+
+    </command>
+    <inputs>
+        <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
+            <option value="denovo">De novo</option>
+            <option value="mapping">Mapping</option>
+        </param>
+        <param name="job_type" type="select" label="Assembly type">
+            <option value="genome">Genome</option>
+            <option value="est">EST (transcriptome)</option>
+        </param>
+        <param name="job_quality" type="select" label="Assembly quality grade">
+            <option value="accurate">Accurate</option>
+            <option value="normal">Normal (deprecated)</option>
+            <option value="draft">Draft</option>
+        </param>
+        <!-- Backbone -->
+        <conditional name="condBackbone">
+           <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
+               <option value="false">No</option>
+               <option value="true">Yes</option>
+           </param>
+           <when value="false" />
+           <when value="true">
+              <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
+              <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
+           </when>
+        </conditional>
+        <!-- Sanger -->
+        <conditional name="condSanger">
+           <param name="use" type="select" label="Sanger/Capillary reads?">
+               <option value="false">No</option>
+               <option value="true">Yes</option>
+           </param>
+           <when value="false" />
+           <when value="true">
+              <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
+           </when>
+        </conditional>
+        <!-- Roche 454 -->
+        <conditional name="condRoche">
+           <param name="use" type="select" label="454 reads?">
+               <option value="false">No</option>
+               <option value="true">Yes</option>
+           </param>
+           <when value="false" />
+           <when value="true">
+              <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
+              <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
+           </when>
+        </conditional>
+        <!-- Illumina -->
+        <conditional name="condIllumina">
+           <param name="use" type="select" label="Solexa/Illumina reads?">
+               <option value="false">No</option>
+               <option value="true">Yes</option>
+           </param>
+           <when value="false" />
+           <when value="true">
+              <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
+           </when>
+        </conditional>
+        <!-- Ion Torrent -->
+        <conditional name="condIonTorrent">
+           <param name="use" type="select" label="Ion Torrent reads?">
+               <option value="false">No</option>
+               <option value="true">Yes</option>
+           </param>
+           <when value="false" />
+           <when value="true">
+              <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
+              <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
+           </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
+        <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
+        <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
+        <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
+        <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
+        <data name="out_log" format="txt" label="MIRA log" />
+    </outputs>
+    <tests>
+            <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
+                 strain data and miraSearchESTSNPs. Here we just assemble it. --> 
+<!--
+Commenting out test until Galaxy framework is fixed,
+https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests
+        <test>
+            <param name="job_method" value="denovo" />
+            <param name="job_type" value="est" />
+            <param name="job_qual" value="accurate" />
+            <param name="condBackbone.use" value="false" />
+            <param name="condSanger.use" value="true" />
+            <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" />
+            <param name="condRoche.use" value="false" />
+            <param name="condIllumina.use" value="false" /> 
+            <param name="condIonTorrent.use" value="false" />
+            <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
+	</test>
+-->
+    </tests>
+    <help>
+
+**What it does**
+
+Runs MIRA v3.4, collects the output, and throws away all the temporary files.
+
+MIRA is an open source assembly tool capable of handling sequence data from
+a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also
+Ion Torrent).
+
+It is particularly suited to small genomes such as bacteria.
+
+**Citation**
+
+If you use this Galaxy tool in work leading to a scientific publication please
+cite the following papers:
+
+Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
+Galaxy tools and workflows for sequence analysis with applications
+in molecular plant pathology. PeerJ 1:e167
+http://dx.doi.org/10.7717/peerj.167
+
+Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999).
+Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
+Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
+http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html
+
+This wrapper is available to install into other Galaxy Instances via the Galaxy
+Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 
+
+    </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira3/tool_dependencies.xml	Thu Jan 30 13:21:21 2014 -0500
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="MIRA" version="3.4.1.1">
+        <install version="1.0">
+            <actions>
+                <!-- Sourceforge doesn't offer nice clean download URLs which is a shame -->      
+                <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_3.4.1.1_prod_linux-gnu_x86_64_static.tar.bz2</action>
+                <action type="move_directory_files">
+                    <source_directory>bin</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+Downloads MIRA v3.4 from Sourceforge, requesting Bastien's precompiled binaries
+for 64bit Linux (x86_64). He also has binaries for 32bit Linux, which we could
+use once the Galaxy installation framework allow that kind of flexibility.
+
+http://chevreux.org/projects_mira.html
+http://sourceforge.net/projects/mira-assembler/
+        </readme>
+    </package>
+</tool_dependency>
+

--- a/tools/mira_3_4/README.rst	Wed Sep 18 06:22:19 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,123 +0,0 @@
-Galaxy tool to wrap the MIRA sequence assembly program (v3.4)
-=============================================================
-
-This tool 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 (MIT licence).
-
-This tool is a short Python script (to collect the MIRA output and move it
-to where Galaxy expects the files, and convert MIRA's TCS file into a tab
-separated file for use in Galaxy).
-
-It is available from the Galaxy Tool Shed at:
-http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 
-
-
-Automated Installation
-======================
-
-This should be straightforward, Galaxy should automatically download and
-install the precompiled binary for MIRA v3.4.0 for the Galaxy wrapper,
-and run any tests.
-
-
-Manual Installation
-===================
-
-There are just two Galaxy files to install:
-
-* mira.py (the Python script)
-* mira.xml (the Galaxy tool definition)
-
-The suggested location is a new tools/mira_3_4 folder. You will also need to
-modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
-this to tools_conf.xml.sample in order to run any tests::
-
-  <tool file="mira_3_4/mira.xml" />
-
-You will also need to install MIRA, we used version 3.4.1.1. See:
-
-* http://chevreux.org/projects_mira.html
-* http://sourceforge.net/projects/mira-assembler/
-
-WARNING: This tool was developed to construct viral genome assembly and
-mapping pipelines, for which the run time and memory requirements are
-negligible. For larger tasks, be aware that MIRA can require vast amounts
-of RAM and run-times of over a week are possible. This tool wrapper makes
-no attempt to spot and reject such large jobs.
-
-
-History
-=======
-
-======= ======================================================================
-Version Changes
-------- ----------------------------------------------------------------------
-v0.0.1  - Initial version (working prototype, using MIRA 3.2.1)
-v0.0.2  - Improve capture of stdout/stderr (should see it as it runs)
-v0.0.3  - Support Ion Torrent reads, now requires MIRA 3.4.0 or later
-          (some other switches changed, e.g. -OUT rrol to rrot, which
-          means the wrapper no longer works with MIRA 3.2.x)
-        - The contig summary file (TCS file) was removed in MIRA 3.4
-        - Report all missing output files (not just first missing one)
-v0.0.4  - Fix problem with backbone arguments inroduced in v0.0.3
-v0.0.5  - Implement the <version_command> tag to record the wrapper
-          version and the MIRA version being used.
-        - Check using MIRA 3.4 (later versions have a different API)
-v0.0.6  - Tell MIRA to use /tmp for temporary files
-        - Tell MIRA to ignore long read names (otherwise it aborts)
-v0.0.7  - Automated installation of the 64 bit Linux MIRA binary.
-v0.0.8  - Basic unit test added (but commented out due to Galaxy issue).
-        - Link to Tool Shed added to help text and this documentation.
-        - Use reStructuredText for this README file.
-        - Adopted standard MIT licence.
-        - Updated citation information (Cock et al. 2013).
-        - Development moved to GitHub, https://github.com/peterjc/pico_galaxy
-======= ======================================================================
-
-
-Developers
-==========
-
-This script and related tools were initially developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-Development has now moved to a dedicated GitHub repository:
-https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4
-
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
-
-    $ tar -czf mira_wrapper.tar.gz tools/mira_3_4/README.rst tools/mira_3_4/mira.xml tools/mira_3_4/mira.py tools/mira_3_4/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta
-
-Check this worked::
-
-    $ tar -tzf mira_wrapper.tar.gz
-    tools/mira_3_4/README.rst
-    tools/mira_3_4/mira.xml
-    tools/mira_3_4/mira.py
-    tools/mira_3_4/tool_dependencies.xml
-    test-data/tvc_mini.fastq
-    test-data/tvc_contigs.fasta
-
-
-Licence (MIT)
-=============
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
-THE SOFTWARE.

--- a/tools/mira_3_4/mira.py	Wed Sep 18 06:22:19 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,124 +0,0 @@
-#!/usr/bin/env python
-"""A simple wrapper script to call MIRA and collect its output.
-"""
-import os
-import sys
-import subprocess
-import shutil
-import time
-
-WRAPPER_VER = "0.0.5" #Keep in sync with the XML file
-
-def stop_err(msg, err=1):
-    sys.stderr.write(msg+"\n")
-    sys.exit(err)
-
-
-def get_version():
-    """Run MIRA to find its version number"""
-    # At the commend line I would use: mira -v | head -n 1
-    # however there is some pipe error when doing that here.
-    try:
-        child = subprocess.Popen(["mira", "-v"],
-                                 stdout=subprocess.PIPE,
-                                 stderr=subprocess.STDOUT)
-    except Exception, err:
-        sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
-        sys.exit(1)
-    ver, tmp = child.communicate()
-    del child
-    return ver.split("\n", 1)[0]
-
-
-mira_ver = get_version()
-if "V3.4." not in mira_ver:
-    stop_err("This wrapper is for MIRA V3.4, not %s" % mira_ver)
-if "-v" in sys.argv:
-    print "MIRA wrapper version %s," % WRAPPER_VER
-    print mira_ver
-    sys.exit(0)
-
-
-def collect_output(temp, name):
-    n3 = (temp, name, name, name)
-    f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
-    if not os.path.isdir(f):
-        stop_err("Missing output folder")
-    if not os.listdir(f):
-        stop_err("Empty output folder")
-    missing = []
-    for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
-                     ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
-                     ("%s/%s_out.wig" % (f, name), out_wig),
-                     ("%s/%s_out.caf" % (f, name), out_caf),
-                     ("%s/%s_out.ace" % (f, name), out_ace)]:
-        if not os.path.isfile(old):
-            missing.append(os.path.splitext(old)[-1])
-        else:
-            shutil.move(old, new)
-    if missing:
-        stop_err("Missing output files: %s" % ", ".join(missing))
-
-def clean_up(temp, name):
-    folder = "%s/%s_assembly" % (temp, name)
-    if os.path.isdir(folder):
-        shutil.rmtree(folder)
-
-#TODO - Run MIRA in /tmp or a configurable directory?
-#Currently Galaxy puts us somewhere safe like:
-#/opt/galaxy-dist/database/job_working_directory/846/
-temp = "."
-name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
-
-start_time = time.time()
-cmd_list =sys.argv[8:]
-cmd = " ".join(cmd_list)
-
-assert os.path.isdir(temp)
-d = "%s_assembly" % name
-assert not os.path.isdir(d), "Path %s already exists" % d
-try:
-    #Check path access
-    os.mkdir(d)
-except Exception, err:
-    sys.stderr.write("Error making directory %s\n%s" % (d, err))
-    sys.exit(1)
-
-#print os.path.abspath(".")
-#print cmd
-
-handle = open(out_log, "w")
-try:
-    #Run MIRA
-    child = subprocess.Popen(cmd_list,
-                             stdout=handle,
-                             stderr=subprocess.STDOUT)
-except Exception, err:
-    sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
-    #TODO - call clean up?
-    handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
-    handle.close()
-    sys.exit(1)
-#Use .communicate as can get deadlocks with .wait(),
-stdout, stderr = child.communicate()
-assert not stdout and not stderr #Should be empty as sent to handle
-run_time = time.time() - start_time
-return_code = child.returncode
-handle.write("\n\nMIRA took %0.2f minutes\n" % (run_time / 60.0))
-print "MIRA took %0.2f minutes" % (run_time / 60.0)
-if return_code:
-    handle.write("Return error code %i from command:\n" % return_code)
-    handle.write(cmd + "\n")
-    handle.close()
-    clean_up(temp, name)
-    stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
-             return_code)
-handle.close()
-
-#print "Collecting output..."
-collect_output(temp, name)
-
-#print "Cleaning up..."
-clean_up(temp, name)
-
-print "Done"

--- a/tools/mira_3_4/mira.xml	Wed Sep 18 06:22:19 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,191 +0,0 @@
-<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.8">
-    <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
-    <requirements>
-        <requirement type="python-module">Bio</requirement>
-        <requirement type="binary">mira</requirement>
-        <requirement type="package" version="3.4.1.1">MIRA</requirement>
-    </requirements>
-    <version_command interpreter="python">mira.py -v</version_command>
-    <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
-##Give the wrapper script list of output filenames, then the mira command...
-mira --job=$job_method,$job_type,$job_quality
-
-##Input files
-#if $condBackbone.use == "true":
-    ## Can this be linked to job_method as well? If mapping we need the backbone...
-    -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
-#end if
-#if $condSanger.use == "true":
-    SANGER_SETTINGS
-    ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
-    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
-    -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
-#end if
-#if $condRoche.use == "true":
-    454_SETTINGS
-    ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
-    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
-    -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
-#end if
-#if $condIllumina.use == "true":
-    SOLEXA_SETTINGS
-    ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
-    -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
-    ##TODO - Look at -LR FASTQ qual offset (fqqo)
-#end if
-#if $condIonTorrent.use == "true":
-    IONTOR_SETTINGS
-    ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
-    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
-    -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
-#end if
-
-##Output files
-COMMON_SETTINGS
-
-##ignore warnings about long read names
--MI:somrnl=0
-
-##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
-##Explicitly disable formats we won't use like MAF (reduce IO)
--OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
-
-##remove_rollover_tmps, remove_tmp_directory
--OUT:rrot=1:rtd=1
-
-##put mira temp directory on local storage                                                                              
--DI:trt=/tmp
-
-    </command>
-    <inputs>
-        <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
-            <option value="denovo">De novo</option>
-            <option value="mapping">Mapping</option>
-        </param>
-        <param name="job_type" type="select" label="Assembly type">
-            <option value="genome">Genome</option>
-            <option value="est">EST (transcriptome)</option>
-        </param>
-        <param name="job_quality" type="select" label="Assembly quality grade">
-            <option value="accurate">Accurate</option>
-            <option value="normal">Normal (deprecated)</option>
-            <option value="draft">Draft</option>
-        </param>
-        <!-- Backbone -->
-        <conditional name="condBackbone">
-           <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
-              <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
-           </when>
-        </conditional>
-        <!-- Sanger -->
-        <conditional name="condSanger">
-           <param name="use" type="select" label="Sanger/Capillary reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
-           </when>
-        </conditional>
-        <!-- Roche 454 -->
-        <conditional name="condRoche">
-           <param name="use" type="select" label="454 reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
-              <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
-           </when>
-        </conditional>
-        <!-- Illumina -->
-        <conditional name="condIllumina">
-           <param name="use" type="select" label="Solexa/Illumina reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
-           </when>
-        </conditional>
-        <!-- Ion Torrent -->
-        <conditional name="condIonTorrent">
-           <param name="use" type="select" label="Ion Torrent reads?">
-               <option value="false">No</option>
-               <option value="true">Yes</option>
-           </param>
-           <when value="false" />
-           <when value="true">
-              <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
-              <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
-           </when>
-        </conditional>
-    </inputs>
-    <outputs>
-        <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" />
-        <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" />
-        <data name="out_caf" format="txt" label="MIRA contigs (CAF)" />
-        <data name="out_ace" format="txt" label="MIRA contigs (ACE)" />
-        <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" />
-        <data name="out_log" format="txt" label="MIRA log" />
-    </outputs>
-    <tests>
-            <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses
-                 strain data and miraSearchESTSNPs. Here we just assemble it. --> 
-<!--
-Commenting out test until Galaxy framework is fixed,
-https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests
-        <test>
-            <param name="job_method" value="denovo" />
-            <param name="job_type" value="est" />
-            <param name="job_qual" value="accurate" />
-            <param name="condBackbone.use" value="false" />
-            <param name="condSanger.use" value="true" />
-            <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" />
-            <param name="condRoche.use" value="false" />
-            <param name="condIllumina.use" value="false" /> 
-            <param name="condIonTorrent.use" value="false" />
-            <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
-	</test>
--->
-    </tests>
-    <help>
-
-**What it does**
-
-Runs MIRA v3.4, collects the output, and throws away all the temporary files.
-
-MIRA is an open source assembly tool capable of handling sequence data from
-a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also
-Ion Torrent).
-
-It is particularly suited to small genomes such as bacteria.
-
-**Citation**
-
-If you use this Galaxy tool in work leading to a scientific publication please
-cite the following papers:
-
-Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013).
-Galaxy tools and workflows for sequence analysis with applications
-in molecular plant pathology. PeerJ 1:e167
-http://dx.doi.org/10.7717/peerj.167
-
-Chevreux et al. (1999).
-Genome Sequence Assembly Using Trace Signals and Additional Sequence Information.
-Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
-
-This wrapper is available to install into other Galaxy Instances via the Galaxy
-Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler 
-
-    </help>
-</tool>

--- a/tools/mira_3_4/tool_dependencies.xml	Wed Sep 18 06:22:19 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="MIRA" version="3.4.1.1">
-        <install version="1.0">
-            <actions>
-                <!-- Sourceforge doesn't offer nice clean download URLs which is a shame -->      
-                <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_3.4.1.1_prod_linux-gnu_x86_64_static.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fmira-assembler%2Ffiles%2FMIRA%2Fstable%2F&amp;ts=1366819213&amp;use_mirror=kent</action>
-                <!-- Currently we only need the main binary itself, mira -->
-                <action type="move_file"><source>mira_3.4.1.1_prod_linux-gnu_x86_64_static/bin/mira</source><destination>$INSTALL_DIR/</destination></action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-Downloads MIRA v3.4 from Sourceforge, requesting Bastien's precompiled binaries
-for 64bit Linux (x86_64). He also has binaries for 32bit Linux, which we could
-use if/when the Galaxy installation framework allow that kind of flexibility.
-
-http://chevreux.org/projects_mira.html
-http://sourceforge.net/projects/mira-assembler/
-        </readme>
-    </package>
-</tool_dependency>
-