# HG changeset patch
# User peterjc
# Date 1324485199 18000
# Node ID 117cce3296afad460dfe201092298db5667970d2
# Parent 298f5c1d9521bb35e5672c1925fd7327f50c15a3
Uploaded wrapper v0.0.3, which is for MIRA v3.4.x which includes support for Ion Torrent.
The Galaxy wrapper will no longer work with MIRA v3.2.x - if you are still using the old version of MIRA, please continue to use v0.0.2 of the wrapper.
diff -r 298f5c1d9521 -r 117cce3296af tools/sr_assembly/mira.py
--- a/tools/sr_assembly/mira.py Tue Jun 21 09:50:32 2011 -0400
+++ b/tools/sr_assembly/mira.py Wed Dec 21 11:33:19 2011 -0500
@@ -11,24 +11,6 @@
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)
f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
@@ -36,16 +18,18 @@
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):
- stop_err("Missing %s output file" % os.path.splitext(old)[-1])
+ missing.append(os.path.splitext(old)[-1])
else:
shutil.move(old, new)
- tcs_to_tabular("%s/%s_assembly/%s_d_results/%s_out.tcs" % n3, out_tcs)
+ if missing:
+ stop_err("Missing output files: %s" % ", ".join(missing))
def clean_up(temp, name):
folder = "%s/%s_assembly" % (temp, name)
@@ -56,14 +40,15 @@
#Currently Galaxy puts us somewhere safe like:
#/opt/galaxy-dist/database/job_working_directory/846/
temp = "."
-name, out_fasta, out_qual, out_tcs, out_ace, out_caf, out_wig, out_log = sys.argv[1:9]
+name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
start_time = time.time()
-cmd = " ".join(sys.argv[9:])
+cmd_list =sys.argv[8:]
+cmd = " ".join(cmd_list)
assert os.path.isdir(temp)
d = "%s_assembly" % name
-assert not os.path.isdir(d)
+assert not os.path.isdir(d), "Path %s already exists" % d
try:
#Check path access
os.mkdir(d)
@@ -77,7 +62,7 @@
handle = open(out_log, "w")
try:
#Run MIRA
- child = subprocess.Popen(sys.argv[9:],
+ child = subprocess.Popen(cmd_list,
stdout=handle,
stderr=subprocess.STDOUT)
except Exception, err:
@@ -102,6 +87,10 @@
return_code)
handle.close()
+#print "Collecting output..."
collect_output(temp, name)
+
+#print "Cleaning up..."
clean_up(temp, name)
+
print "Done"
diff -r 298f5c1d9521 -r 117cce3296af tools/sr_assembly/mira.txt
--- a/tools/sr_assembly/mira.txt Tue Jun 21 09:50:32 2011 -0400
+++ b/tools/sr_assembly/mira.txt Wed Dec 21 11:33:19 2011 -0500
@@ -7,7 +7,7 @@
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:
+separated file for use in Galaxy). There are just two files to install:
* mira.py (the Python script)
* mira.xml (the Galaxy tool definition)
@@ -16,9 +16,9 @@
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:
-
+
-You will also need to install MIRA, we used version 3.2.1. See:
+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/
@@ -33,8 +33,13 @@
History
=======
-v0.0.1 - Initial version (working prototype)
+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 switched 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)
Developers
diff -r 298f5c1d9521 -r 117cce3296af tools/sr_assembly/mira.xml
--- a/tools/sr_assembly/mira.xml Tue Jun 21 09:50:32 2011 -0400
+++ b/tools/sr_assembly/mira.xml Wed Dec 21 11:33:19 2011 -0500
@@ -1,40 +1,46 @@
-
- Takes Sanger, Roche, and Illumina data
- mira.py mira $out_fasta $out_qual $out_tcs $out_ace $out_caf $out_wig $out_log
+
+ Takes Sanger, Roche, Illumina, and Ion Torrent data
+ 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 $condBackbone.use == "true":
## Can this be linked to job_method as well? If mapping we need the backbone...
- -SB:lb=yes -SB:bft=fasta -FN:bbin=${condBackbone.filename}
+ -SB:lb=1:bft=1 -FN:bbin=${condBackbone.filename}
#end if
#if $condSanger.use == "true":
- Sanger_SETTINGS
- ## Not easy to add sanger to --job, so use load_sequence_data(lsd) instead
- -LR:lsd=yes
+ SANGER_SETTINGS
+ ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
- -LR:mxti=no -LR:ft=fastq -FN:fqi=${condSanger.filename}
+ -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
#end if
#if $condRoche.use == "true":
454_SETTINGS
- ## Not easy to add 454 to --job, so use load_sequence_data(lsd) instead
- -LR:lsd=yes
+ ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
- -LR:mxti=no -LR:ft=fastq -FN:fqi=${condRoche.filename}
+ -LR:lsd=1:mxti=0: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}
+ ## 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
-##remove_rollover_logs, remove_log_directory
--OUT:rrol=yes -OUT:rld=yes
+##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
@@ -47,9 +53,9 @@
-
+
+
-
@@ -82,7 +88,8 @@
-
+
+
@@ -96,11 +103,22 @@
+
+
+
+
+
+
+
+
+
+
+
+
-
@@ -117,9 +135,6 @@
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