--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/sr_assembly/mira.py	Tue Jun 07 16:23:51 2011 -0400
@@ -0,0 +1,80 @@
+#!/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
+
+def stop_err(msg, err=1):
+    sys.stderr.write(msg+"\n")
+    sys.exit(err)
+
+def tcs_to_tabular(old, new):
+    in_handle = open(old, "rU")
+    out_handle = open(new, "w")
+    assert in_handle.readline() == "#TCS V1.0\n"
+    assert in_handle.readline() == "#\n"
+    assert in_handle.readline() == "# contig name          padPos  upadPos | B  Q | tcov covA covC covG covT cov* | qA qC qG qT q* |  S | Tags\n"
+    assert in_handle.readline() == "#\n"
+    out_handle.write("#%s\n" % "\t".join(["contig", "pasPos", "upadPos", "B", "Q",
+                                         "tcov", "covA", "covC", "covG", "covT", "cov*",
+                                         "qA", "qC", "qG", "qT", "q*", "S", "Tags"]))
+    for line in in_handle:
+        parts = line.rstrip("\n").split(None,22)
+        assert parts[3] == parts[6] == parts[13] == parts[19] == parts[21] == "|"
+        wanted = parts[:3] + parts[4:6]+parts[7:13]+parts[14:19]+parts[20:21]+parts[22:]
+        out_handle.write("%s\n" % "\t".join(wanted))
+    out_handle.close()
+    in_handle.close()
+
+def collect_output(temp, name):
+    n3 = (temp, name, name, name)
+    tcs_to_tabular("%s/%s_assembly/%s_d_results/%s_out.tcs" % n3, out_tcs)
+    for old, new in [("%s/%s_assembly/%s_d_results/%s_out.unpadded.fasta" % n3, out_fasta),
+                     ("%s/%s_assembly/%s_d_results/%s_out.unpadded.fasta.qual" % n3, out_qual),
+                     ("%s/%s_assembly/%s_d_results/%s_out.wig" % n3, out_wig),
+                     ("%s/%s_assembly/%s_d_results/%s_out.caf" % n3, out_caf),
+                     ("%s/%s_assembly/%s_d_results/%s_out.ace" % n3, out_ace)]:
+        if not os.path.isfile(old):
+            stop_err("Missing %s output file" % os.path.splitext(old)[-1])
+        else:
+            shutil.move(old, new)
+
+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?
+temp = "."
+name, out_fasta, out_qual, out_tcs, out_ace, out_caf, out_wig, out_log = sys.argv[1:9]
+start_time = time.time()
+try:
+    cmd = " ".join(sys.argv[9:])
+    child = subprocess.Popen(sys.argv[9:],
+                             stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+except Exception, err:
+    sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
+    sys.exit(1)
+#Use .communicate as can get deadlocks with .wait(),
+stdout, stderr = child.communicate()
+run_time = time.time() - start_time
+return_code = child.returncode
+handle = open(out_log, "w")
+handle.write(stdout)
+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()
+
+collect_output(temp, name)
+clean_up(temp, name)
+print "Done"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/sr_assembly/mira.txt	Tue Jun 07 16:23:51 2011 -0400
@@ -0,0 +1,77 @@
+Galaxy tool to wrap the MIRA sequence assembly program
+======================================================
+
+This tool 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 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
+separate file for use in Galaxy). There are just two files to install:
+
+* mira.py (the Python script)
+* mira.xml (the Galaxy tool definition)
+
+The suggested location is the tools/sr_assembly 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="sr_assembly/seq_primer_clip.xml" />
+
+You will also need to install MIRA, we used version 3.2.1. 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
+=======
+
+v0.0.1 - Initial version (working prototype)
+
+
+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 mira_wrapper.tar.gz tools/sr_assembly/mira.*
+
+Check this worked:
+
+$ tar -tzf mira_wrapper.tar.gz
+tools/sr_assembly/mira.py
+tools/sr_assembly/mira.txt
+tools/sr_assembly/mira.xml
+
+
+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.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/sr_assembly/mira.xml	Tue Jun 07 16:23:51 2011 -0400
@@ -0,0 +1,131 @@
+<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.1">
+    <description>Takes Sanger, Roche, and Illumina data</description>
+	<command interpreter="python">mira.py mira $out_fasta $out_qual $out_tcs $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 $condBackbone.use == "true":
+    ## Can this be linked to job_method as well? If mapping we need the backbone...
+    -SB:lb=yes -SB:bft=fasta -FN:bbin=${condBackbone.filename}
+#end if
+#if $condSanger.use == "true":
+    Sanger_SETTINGS
+    ## Not easy to add sanger to --job, so use load_sequence_data(lsd) instead
+    -LR:lsd=yes
+    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+    -LR:mxti=no -LR:ft=fastq -FN:fqi=${condSanger.filename}
+#end if
+#if $condRoche.use == "true":
+    454_SETTINGS
+    ## Not easy to add 454 to --job, so use load_sequence_data(lsd) instead
+    -LR:lsd=yes
+    ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+    -LR:mxti=no -LR:ft=fastq -FN:fqi=${condRoche.filename}
+#end if
+#if $condIllumina.use == "true":
+    SOLEXA_SETTINGS
+    ## Not easy to add solexa to --job, so use load_sequence_data(lsd) instead
+    -LR:lsd=yes -LR:ft=fastq -FN:fgi=${condIllumina.filename}
+    ##TODO - Look at -LR FASTQ qual offset (fqqo)
+#end if
+
+
+##Output files
+COMMON_SETTINGS
+##remove_rollover_logs, remove_log_directory
+-OUT:rrol=yes -OUT:rld=yes
+
+    </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="normal">Normal</option>
+            <option value="draft">Draft</option>
+            <option value="accurate">Accurate</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">
+              <param name="filename" type="data" format="fastq,sff" 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>
+	</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_tcs" format="tabular" label="MIRA contigs summary" />
+	    <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>
+	</tests>
+	<requirements>
+		<requirement type="python-module">Bio</requirement>
+	</requirements>
+	<help>
+
+**What it does**
+
+Runs MIRA v3, collects the output, and throws away all the temporary files.
+
+The MIRA transposed contig summary (TCS) file is converted into a tabular file for use within Galaxy.
+This records one line per base per contig, and including things like the base, quality, coverage and any tags.
+
+**Citation**
+
+This tool uses MIRA. If you use this tool in scientific work leading to a
+publication, please cite:
+
+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.
+
+	</help>
+</tool>