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changeset 3:c1419fa820c6 draft

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Uploaded
author devteam
date Wed, 18 Mar 2015 15:44:51 -0400
parents c09a20532957
children af7c50162f0b
files bam_to_sam.py bam_to_sam.xml macros.xml tool_dependencies.xml
diffstat 4 files changed, 65 insertions(+), 186 deletions(-) [+]
line wrap: on
line diff
--- a/bam_to_sam.py	Thu Mar 05 21:22:11 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,129 +0,0 @@
-#!/usr/bin/env python
-"""
-Converts BAM data to sorted SAM data.
-usage: bam_to_sam.py [options]
-   --input1: SAM file to be converted
-   --output1: output dataset in bam format
-"""
-
-import optparse, os, sys, subprocess, tempfile, shutil
-from galaxy import eggs
-import pkg_resources; pkg_resources.require( "bx-python" )
-from bx.cookbook import doc_optparse
-#from galaxy import util
-
-def stop_err( msg ):
-    sys.stderr.write( '%s\n' % msg )
-    sys.exit()
-
-def __main__():
-    #Parse Command Line
-    parser = optparse.OptionParser()
-    parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' )
-    parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' )
-    parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' )
-    ( options, args ) = parser.parse_args()
-
-    # output version # of tool
-    try:
-        tmp = tempfile.NamedTemporaryFile().name
-        tmp_stdout = open( tmp, 'wb' )
-        proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
-        tmp_stdout.close()
-        returncode = proc.wait()
-        stdout = None
-        for line in open( tmp_stdout.name, 'rb' ):
-            if line.lower().find( 'version' ) >= 0:
-                stdout = line.strip()
-                break
-        if stdout:
-            sys.stdout.write( 'Samtools %s\n' % stdout )
-        else:
-            raise Exception
-    except:
-        sys.stdout.write( 'Could not determine Samtools version\n' )
-
-    tmp_dir = tempfile.mkdtemp( dir='.' )
-
-    try:
-        # exit if input file empty
-        if os.path.getsize( options.input1 ) == 0:
-            raise Exception, 'Initial BAM file empty'
-        # Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created. This command
-        # may also create temporary files <out.prefix>.%d.bam when the whole alignment cannot be fitted
-        # into memory ( controlled by option -m ).
-        tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
-        tmp_sorted_aligns_file_base = tmp_sorted_aligns_file.name
-        tmp_sorted_aligns_file_name = '%s.bam' % tmp_sorted_aligns_file.name
-        tmp_sorted_aligns_file.close()
-        command = 'samtools sort %s %s' % ( options.input1, tmp_sorted_aligns_file_base )
-        tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
-        tmp_stderr = open( tmp, 'wb' )
-        proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
-        returncode = proc.wait()
-        tmp_stderr.close()
-        # get stderr, allowing for case where it's very large
-        tmp_stderr = open( tmp, 'rb' )
-        stderr = ''
-        buffsize = 1048576
-        try:
-            while True:
-                stderr += tmp_stderr.read( buffsize )
-                if not stderr or len( stderr ) % buffsize != 0:
-                    break
-        except OverflowError:
-            pass
-        tmp_stderr.close()
-        if returncode != 0:
-            raise Exception, stderr
-        # exit if sorted BAM file empty
-        if os.path.getsize( tmp_sorted_aligns_file_name) == 0:
-            raise Exception, 'Intermediate sorted BAM file empty'
-    except Exception, e:
-        #clean up temp files
-        if os.path.exists( tmp_dir ):
-            shutil.rmtree( tmp_dir )
-        stop_err( 'Error sorting alignments from (%s), %s' % ( options.input1, str( e ) ) )
-
-
-    try:
-        # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ).
-        if options.header:
-            view_options = "-h"
-        else:
-            view_options = ""
-        command = 'samtools view %s -o %s %s' % ( view_options, options.output1, tmp_sorted_aligns_file_name )
-        tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
-        tmp_stderr = open( tmp, 'wb' )
-        proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
-        returncode = proc.wait()
-        tmp_stderr.close()
-        # get stderr, allowing for case where it's very large
-        tmp_stderr = open( tmp, 'rb' )
-        stderr = ''
-        buffsize = 1048576
-        try:
-            while True:
-                stderr += tmp_stderr.read( buffsize )
-                if not stderr or len( stderr ) % buffsize != 0:
-                    break
-        except OverflowError:
-            pass
-        tmp_stderr.close()
-        if returncode != 0:
-            raise Exception, stderr
-    except Exception, e:
-        #clean up temp files
-        if os.path.exists( tmp_dir ):
-            shutil.rmtree( tmp_dir )
-        stop_err( 'Error extracting alignments from (%s), %s' % ( options.input1, str( e ) ) )
-    #clean up temp files
-    if os.path.exists( tmp_dir ):
-        shutil.rmtree( tmp_dir )
-    # check that there are results in the output file
-    if os.path.getsize( options.output1 ) > 0:
-        sys.stdout.write( 'BAM file converted to SAM' )
-    else:
-        stop_err( 'The output file is empty, there may be an error with your input file.' )
-
-if __name__=="__main__": __main__()
--- a/bam_to_sam.xml	Thu Mar 05 21:22:11 2015 -0500
+++ b/bam_to_sam.xml	Wed Mar 18 15:44:51 2015 -0400
@@ -1,63 +1,50 @@
-<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.4">
-  <requirements>
-    <requirement type="package" version="0.1.19">samtools</requirement>
-  </requirements>
-  <description>converts BAM format to SAM format</description>
-  <command interpreter="python">
-    bam_to_sam.py
-      --input1=$input1
-      --output1=$output1
-      $header
-  </command>
-  <inputs>
-    <param name="input1" type="data" format="bam" label="BAM File to Convert" />
-    <param name="header" type="boolean" truevalue="--header" falsevalue="" checked="False" label="Include header in output" />
-  </inputs>
-  <outputs>
-    <data format="sam" name="output1" label="${tool.name} on ${on_string}: converted SAM" />
-  </outputs>
-  <tests>
-    <test>
-      <!--
-      Bam-to-Sam command:
-      samtools view -o bam_to_sam_out1.sam test-data/bam_to_sam_in1.bam
-      bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
-      -->
-      <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
-      <param name="header" value="" />
-      <output name="output1" file="bam_to_sam_out1.sam" sorted="True" />
-    </test>
-    <test>
-      <!--
-      Bam-to-Sam command:
-      samtools view -o bam_to_sam_out2.sam test-data/bam_to_sam_in2.bam
-      bam_to_sam_in2.bam can be created from bam_to_sam_in2.sam
-      -->
-      <param name="input1" value="bam_to_sam_in2.bam" ftype="bam" />
-      <param name="header" value="" />
-      <output name="output1" file="bam_to_sam_out2.sam" sorted="True" />
-    </test>
-    <test>
-      <!--
-      Bam-to-Sam command:
-      samtools view -h -o bam_to_sam_out3.sam test-data/bam_to_sam_in1.bam
-      bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
-      -->
-      <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
-      <param name="header" value="--header" />
-      <output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /><!-- header param not working in func tests so won't produce correct 6-line header (fine in browser) -->
-    </test>
-  </tests>
-  <help>
+<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.6">
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="version_command"></expand>
+  <expand macro="stdio"></expand>
+  <description>converts BAM format to SAM format</description>  
+    <command>
+<![CDATA[
+  samtools sort -O bam -@ \${GALAXY_SLOTS:-1} "$input1" -o sorted_input.bam -T temp && 
+  samtools view sorted_input.bam $header -o $output1 -@ \${GALAXY_SLOTS:-1}
+]]>
+    </command>
+    <inputs>
+        <param format="bam" label="BAM File to Convert" name="input1" type="data" />
+        <param checked="False" falsevalue="" label="Include header in output" name="header" truevalue="-h" type="boolean" />
+    </inputs>
+    <outputs>
+        <data format="sam" label="${tool.name} on ${on_string}: converted SAM" name="output1" />
+    </outputs>
+    <tests>
+        <test>
+            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
+            <param name="header" value="" />
+            <output file="bam_to_sam_out1.sam" name="output1" sorted="True" />
+        </test>
+        <test>
+            <param ftype="bam" name="input1" value="bam_to_sam_in2.bam" />
+            <param name="header" value="" />
+            <output file="bam_to_sam_out2.sam" name="output1" sorted="True" />
+        </test>
+        <test>
+            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
+            <param name="header" value="True" />
+            <output file="bam_to_sam_out3.sam" name="output1" sorted="True" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
 
 **What it does**
 
 This tool uses the SAMTools_ toolkit to produce a SAM file from a BAM file.
 
 .. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
-
+]]>
   </help>
-  <citations>
-      <citation type="doi">10.1093/bioinformatics/btp352</citation>
-  </citations>
+  <expand macro="citations"></expand>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Mar 18 15:44:51 2015 -0400
@@ -0,0 +1,21 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.2">samtools</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/btp352</citation>
+        </citations>
+    </xml>
+    <xml name="version_command">
+        <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" level="fatal" description="Error" />
+        </stdio>
+    </xml>
+</macros>
--- a/tool_dependencies.xml	Thu Mar 05 21:22:11 2015 -0500
+++ b/tool_dependencies.xml	Wed Mar 18 15:44:51 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="samtools" version="0.1.19">
-        <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>