# HG changeset patch
# User peterjc
# Date 1402409518 14400
# Node ID aeb3e35f823676c6cdaf34b04e8273b22b6d83df
# Parent  8487d70e82aaf0b73c0bb99b16fb6c8ff558dd32
Uploaded v0.0.4 preview, made MAF and BAM output optional

diff -r 8487d70e82aa -r aeb3e35f8236 tools/mira4/README.rst
--- a/tools/mira4/README.rst	Wed May 21 06:56:06 2014 -0400
+++ b/tools/mira4/README.rst	Tue Jun 10 10:11:58 2014 -0400
@@ -91,6 +91,8 @@
           (``$TMPDIR``, ``$TEMP``, or ``$TMP`` in that order). This was
           previously hard coded as ``/tmp``.
 v0.0.3  - Updated to target MIRA 4.0.2
+v0.0.4  - Using optparse for the Python wrapper script API
+        - Made MAF and BAM outputs optional
 ======= ======================================================================
 
 
diff -r 8487d70e82aa -r aeb3e35f8236 tools/mira4/mira4.py
--- a/tools/mira4/mira4.py	Wed May 21 06:56:06 2014 -0400
+++ b/tools/mira4/mira4.py	Tue Jun 10 10:11:58 2014 -0400
@@ -7,11 +7,12 @@
 import shutil
 import time
 import tempfile
+from optparse import OptionParser
 
 #Do we need any PYTHONPATH magic?
 from mira4_make_bam import make_bam
 
-WRAPPER_VER = "0.0.1" #Keep in sync with the XML file
+WRAPPER_VER = "0.0.4" #Keep in sync with the XML file
 
 def stop_err(msg, err=1):
     sys.stderr.write(msg+"\n")
@@ -34,6 +35,35 @@
     del child
     return ver.split("\n", 1)[0].strip()
 
+#Parse Command Line
+usage = """Galaxy MIRA4 wrapper script v%s - use as follows:
+
+$ python mira4.py ...
+
+This will run the MIRA binary and collect its output files as directed.
+""" % WRAPPER_VER
+parser = OptionParser(usage=usage)
+parser.add_option("-m", "--manifest", dest="manifest",
+                  default=None, metavar="FILE",
+                  help="MIRA manifest filename")
+parser.add_option("--maf", dest="maf",
+                  default="-", metavar="FILE",
+                  help="MIRA MAF output filename")
+parser.add_option("--bam", dest="bam",
+                  default="-", metavar="FILE",
+                  help="Unpadded BAM output filename")
+parser.add_option("--fasta", dest="fasta",
+                  default="-", metavar="FILE",
+                  help="Unpadded FASTA output filename")
+parser.add_option("--log", dest="log",
+                  default="-", metavar="FILE",
+                  help="MIRA logging output filename")
+options, args = parser.parse_args()
+manifest = options.manifest
+out_maf = options.maf
+out_bam = options.bam
+out_fasta = options.fasta
+out_log = options.log
 
 try:
     mira_path = os.environ["MIRA4"]
@@ -60,6 +90,11 @@
         print "WARNING: miraconvert %s" % mira_convert_ver
     sys.exit(0)
 
+if not manifest:
+    stop_err("Manifest is required")
+elif not os.path.isfile(manifest):
+    stop_err("Missing input MIRA manifest file: %r" % manifest)
+
 
 try:
     threads = int(os.environ.get("GALAXY_SLOTS", "1"))
@@ -143,6 +178,8 @@
                      (old_fasta, out_fasta)]:
         if not os.path.isfile(old):
             missing = True
+        elif not new or new == "-":
+            handle.write("Ignoring %s\n" % old)
         else:
             handle.write("Capturing %s\n" % old)
             shutil.move(old, new)
@@ -154,9 +191,10 @@
 
     #For mapping mode, probably most people would expect a BAM file
     #using the reference FASTA file...
-    msg = make_bam(mira_convert, out_maf, ref_fasta, out_bam, handle)
-    if msg:
-        stop_err(msg)
+    if out_bam and out_bam != "-":
+        msg = make_bam(mira_convert, out_maf, ref_fasta, out_bam, handle)
+        if msg:
+            stop_err(msg)
 
 def clean_up(temp, name):
     folder = "%s/%s_assembly" % (temp, name)
@@ -167,14 +205,12 @@
 #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]
+
 name = "MIRA"
-manifest, out_maf, out_bam, out_fasta, out_log = sys.argv[1:]
 
 override_temp(manifest)
 
 start_time = time.time()
-#cmd_list =sys.argv[8:]
 cmd_list = [mira_binary, "-t", str(threads), manifest]
 cmd = " ".join(cmd_list)
 
@@ -192,7 +228,10 @@
 #print os.path.abspath(".")
 #print cmd
 
-handle = open(out_log, "w")
+if out_log and out_log != "-":
+    handle = open(out_log, "w")
+else:
+    handle = open(os.devnull, "w")
 handle.write("======================== MIRA manifest (instructions) ========================\n")
 m = open(manifest, "rU")
 for line in m:
diff -r 8487d70e82aa -r aeb3e35f8236 tools/mira4/mira4_de_novo.xml
--- a/tools/mira4/mira4_de_novo.xml	Wed May 21 06:56:06 2014 -0400
+++ b/tools/mira4/mira4_de_novo.xml	Tue Jun 10 10:11:58 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.3">
+<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.4">
     <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
     <requirements>
         <requirement type="binary">mira</requirement>
@@ -8,8 +8,16 @@
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
     <version_command interpreter="python">mira4.py --version</version_command>
-    <command interpreter="python">
-mira4.py "$manifest" "$out_maf" "$out_bam" "$out_fasta" "$out_log"
+    <command interpreter="python">mira4.py
+--manifest "$manifest"
+#if str($maf_wanted)=="true":
+--maf "$out_maf"
+#end if
+#if str($bam_wanted)=="true":
+--bam "$out_bam"
+#end if
+--fasta "$out_fasta"
+--log "$out_log"
     </command>
     <stdio>
         <!-- Assume anything other than zero is an error -->
@@ -67,12 +75,18 @@
             <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)"
                   help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
         </repeat>
+        <param name="maf_wanted" type="boolean" label="Output assembly in MIRA's own format?" checked="False" />
+        <param name="bam_wanted" type="boolean" label="Convert assembly into BAM format?" checked="True" />
     </inputs>
     <code file="mira4_validator.py" />
     <outputs>
         <data name="out_fasta" format="fasta" label="MIRA de novo contigs (FASTA)" />
-        <data name="out_bam" format="bam" label="MIRA de novo assembly (BAM)" />
-        <data name="out_maf" format="mira" label="MIRA de novo assembly" />
+        <data name="out_bam" format="bam" label="MIRA de novo assembly (BAM)">
+            <filter>bam_wanted is True</filter>
+        </data>
+        <data name="out_maf" format="mira" label="MIRA de novo assembly">
+            <filter>maf_wanted is True</filter>
+        </data>
         <!-- TODO?
         <data name="out_contigstats" format="tabular" label="MIRA contig stats" />
         -->
@@ -162,6 +176,8 @@
             <param name="technology" value="sanger" />
             <param name="type" value="none" />
             <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" />
+            <param name="maf_wanted" value="true"/>
+            <param name="bam_wanted" value="true"/>
             <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" />
             <output name="out_bam" file="empty_file.dat" compare="contains" />
             <output name="out_maf" file="empty_file.dat" compare="contains" />
@@ -176,6 +192,8 @@
             <param name="job_quality" value="accurate" />
             <param name="type" value="none" />
             <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" />
+            <param name="maf_wanted" value="true"/>
+            <param name="bam_wanted" value="true"/>
             <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" />
             <output name="out_bam" file="empty_file.dat" compare="contains" />
             <output name="out_maf" file="empty_file.dat" compare="contains" />
diff -r 8487d70e82aa -r aeb3e35f8236 tools/mira4/mira4_mapping.xml
--- a/tools/mira4/mira4_mapping.xml	Wed May 21 06:56:06 2014 -0400
+++ b/tools/mira4/mira4_mapping.xml	Tue Jun 10 10:11:58 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.3">
+<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.4">
     <description>Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description>
     <requirements>
         <requirement type="binary">mira</requirement>
@@ -8,8 +8,16 @@
         <requirement type="package" version="0.1.19">samtools</requirement>
     </requirements>
     <version_command interpreter="python">mira4.py --version</version_command>
-    <command interpreter="python">
-mira4.py "$manifest" "$out_maf" "$out_bam" "$out_fasta" "$out_log"
+    <command interpreter="python">mira4.py
+--manifest "$manifest"
+#if str($maf_wanted) == "true":
+--maf "$out_maf"
+#end if
+#if str($bam_wanted) == "true":
+--bam "$out_bam"
+#end if
+--fasta "$out_fasta"
+--log "$out_log"
     </command>
     <stdio>
         <!-- Assume anything other than zero is an error -->
@@ -69,11 +77,17 @@
             <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)"
                    help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." />
         </repeat>
+        <param name="maf_wanted" type="boolean" label="Output mapping in MIRA's own format?" checked="False" />
+        <param name="bam_wanted" type="boolean" label="Convert mapping into BAM format?" checked="True" />
     </inputs>
     <outputs>
         <data name="out_fasta" format="fasta" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping contigs (FASTA)" />
-        <data name="out_bam" format="bam" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly (BAM)" />
-        <data name="out_maf" format="mira" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly" />
+        <data name="out_bam" format="bam" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly (BAM)">
+            <filter>bam_wanted is True</filter>
+        </data>
+        <data name="out_maf" format="mira" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping assembly">
+            <filter>maf_wanted is True</filter>
+        </data>
         <data name="out_log" format="txt" label="MIRA #if str($strain_setup)=='same' then 'same strain' else 'reference' # mapping log" />
     </outputs>
     <configfiles>
@@ -168,6 +182,8 @@
             <param name="strain_setup" value="default" />
             <param name="type" value="none" />
             <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" />
+            <param name="maf_wanted" value="true"/>
+            <param name="bam_wanted" value="true"/>
             <output name="out_fasta" file="tvc_map_ref_strain.fasta" ftype="fasta" />
             <output name="out_bam" file="empty_file.dat" compare="contains" />
             <output name="out_maf" file="empty_file.dat" compare="contains" />
@@ -180,6 +196,8 @@
             <param name="strain_setup" value="same" />
             <param name="type" value="none" />
             <param name="filenames" value="tvc_mini.fastq" ftype="fastqsanger" />
+            <param name="maf_wanted" value="true"/>
+            <param name="bam_wanted" value="true"/>
             <output name="out_fasta" file="tvc_map_same_strain.fasta" ftype="fasta" />
             <output name="out_bam" file="empty_file.dat" compare="contains" />
             <output name="out_maf" file="empty_file.dat" compare="contains" />
diff -r 8487d70e82aa -r aeb3e35f8236 tools/mira4/repository_dependencies.xml
--- a/tools/mira4/repository_dependencies.xml	Wed May 21 06:56:06 2014 -0400
+++ b/tools/mira4/repository_dependencies.xml	Tue Jun 10 10:11:58 2014 -0400
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories description="This requires the MIRA datatype definitions (e.g. the MIRA Assembly Format).">
-    <repository changeset_revision="29ff2a2b6eaa" name="mira_datatypes" owner="peterjc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="29ff2a2b6eaa" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>
diff -r 8487d70e82aa -r aeb3e35f8236 tools/mira4/tool_dependencies.xml
--- a/tools/mira4/tool_dependencies.xml	Wed May 21 06:56:06 2014 -0400
+++ b/tools/mira4/tool_dependencies.xml	Tue Jun 10 10:11:58 2014 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="MIRA" version="4.0">
         <install version="1.0">