changeset 8:4266cccbb45a draft

Uploaded v0.0.7 take 2, fixed path in installation

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira_3_4/mira.py	Wed Apr 24 12:43:17 2013 -0400
@@ -0,0 +1,124 @@
+#!/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"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira_3_4/mira.txt	Wed Apr 24 12:43:17 2013 -0400
@@ -0,0 +1,104 @@
+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.
+
+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).
+
+
+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
+=======
+
+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.
+
+
+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 mira_wrapper.tar.gz tools/mira_3_4/mira.*
+
+Check this worked:
+
+$ tar -tzf mira_wrapper.tar.gz
+tools/mira_3_4/mira.py
+tools/mira_3_4/mira.txt
+tools/mira_3_4/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/mira_3_4/mira.xml	Wed Apr 24 12:43:17 2013 -0400
@@ -0,0 +1,155 @@
+<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.6">
+    <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
+	<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>
+	</tests>
+	<requirements>
+		<requirement type="python-module">Bio</requirement>
+		<requirement type="binary">mira</requirement>
+	</requirements>
+	<help>
+
+**What it does**
+
+Runs MIRA v3.4, collects the output, and throws away all the temporary files.
+
+**Citation**
+
+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>

--- a/tools/sr_assembly/mira.py	Thu Feb 14 06:26:32 2013 -0500
+++ /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/sr_assembly/mira.txt	Thu Feb 14 06:26:32 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-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
-separated 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/mira.xml" />
-
-You will also need to install MIRA, we used version 3.4.0. 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, 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)
-
-
-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
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-OR PERFORMANCE OF THIS SOFTWARE.

--- a/tools/sr_assembly/mira.xml	Thu Feb 14 06:26:32 2013 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,156 +0,0 @@
-<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.6">
-    <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description>
-	<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>
-	</tests>
-	<requirements>
-		<requirement type="python-module">Bio</requirement>
-		<requirement type="binary">mira</requirement>
-	</requirements>
-	<help>
-
-**What it does**
-
-Runs MIRA v3, collects the output, and throws away all the temporary files.
-
-**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>