# HG changeset patch
# User devteam
# Date 1444755220 14400
# Node ID 3bade5114f215bca9d3aa5fb9cd7ea580fe76d41
# Parent  ad3c355b82491fef2a4997276db1fc40eae941fa
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734

diff -r ad3c355b8249 -r 3bade5114f21 bam_to_sam.py
--- a/bam_to_sam.py	Wed Mar 04 22:28:17 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__()
diff -r ad3c355b8249 -r 3bade5114f21 bam_to_sam.xml
--- a/bam_to_sam.xml	Wed Mar 04 22:28:17 2015 -0500
+++ b/bam_to_sam.xml	Tue Oct 13 12:53:40 2015 -0400
@@ -1,63 +1,54 @@
-<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 ${on_string}: converted SAM" />
-  </outputs>
-  <tests>
-    <test>
-      <!--
-      Bam-to-Sam command:
-      samtools view -o bam_to_sam_out1.sam test-data/bam_to_sam_in1.bam
-      bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
-      -->
-      <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
-      <param name="header" value="" />
-      <output name="output1" file="bam_to_sam_out1.sam" sorted="True" />
-    </test>
-    <test>
-      <!--
-      Bam-to-Sam command:
-      samtools view -o bam_to_sam_out2.sam test-data/bam_to_sam_in2.bam
-      bam_to_sam_in2.bam can be created from bam_to_sam_in2.sam
-      -->
-      <param name="input1" value="bam_to_sam_in2.bam" ftype="bam" />
-      <param name="header" value="" />
-      <output name="output1" file="bam_to_sam_out2.sam" sorted="True" />
-    </test>
-    <test>
-      <!--
-      Bam-to-Sam command:
-      samtools view -h -o bam_to_sam_out3.sam test-data/bam_to_sam_in1.bam
-      bam_to_sam_in1.bam can be created from bam_to_sam_in1.sam
-      -->
-      <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" />
-      <param name="header" value="--header" />
-      <output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /><!-- header param not working in func tests so won't produce correct 6-line header (fine in browser) -->
-    </test>
-  </tests>
-  <help>
+<tool id="bam_to_sam" name="BAM-to-SAM" version="2.0">
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"></expand>
+  <expand macro="version_command"></expand>
+  <expand macro="stdio"></expand>
+  <description>convert BAM to SAM</description>  
+    <command>
+<![CDATA[
+  samtools view -o "${output1}" ${header} "${input1}"
+]]>
+    </command>
+    <inputs>
+        <param format="bam" label="BAM File to Convert" name="input1" type="data" />
+        <param name="header" label="Header options" type="select" help="Allows to choose between seeing the entire dataset with the header, header only, or data only.">
+          <option value="-h">Include header in SAM output (-h)</option>
+          <option value="-H">Print header only (-H)</option>
+          <option value="">Exclude header</option>
+        </param>
+    </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="-h" />
+            <output file="bam_to_sam_out1.sam" name="output1" sorted="True" />
+        </test>
+        <test>
+            <param ftype="bam" name="input1" value="bam_to_sam_in1.bam" />
+            <param name="header" value="-H" />
+            <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="" />
+            <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.
+Converts BAM dataset to SAM using ``samtools view`` command::
 
-.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml
+ samtools view -o [OUTPUT SAM] [-h|-H] [INPUT BAM] 
 
+]]>
   </help>
-  <citations>
-      <citation type="doi">10.1093/bioinformatics/btp352</citation>
-  </citations>
+  <expand macro="citations"></expand>
 </tool>
diff -r ad3c355b8249 -r 3bade5114f21 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Oct 13 12:53:40 2015 -0400
@@ -0,0 +1,70 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.2">samtools</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">
+                @misc{SAM_def,
+                title={Definition of SAM/BAM format},
+                url = {https://samtools.github.io/hts-specs/SAMv1.pdf},}
+            </citation>
+            <citation type="doi">10.1093/bioinformatics/btp352</citation>
+            <citation type="doi">10.1093/bioinformatics/btr076</citation>
+            <citation type="doi">10.1093/bioinformatics/btr509</citation>
+            <citation type="bibtex">
+                @misc{Danecek_et_al,
+                Author={Danecek, P., Schiffels, S., Durbin, R.},
+                title={Multiallelic calling model in bcftools (-m)},
+                url = {http://samtools.github.io/bcftools/call-m.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{Durbin_VCQC,
+                Author={Durbin, R.},
+                title={Segregation based metric for variant call QC},
+                url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{Li_SamMath,
+                Author={Li, H.},
+                title={Mathematical Notes on SAMtools Algorithms},
+                url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},}
+            </citation>
+            <citation type="bibtex">
+                @misc{SamTools_github,
+                title={SAMTools GitHub page},
+                url = {https://github.com/samtools/samtools},}
+            </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>
+    <token name="@no-chrom-options@">
+-----
+
+.. class:: warningmark
+
+**No options available? How to re-detect metadata**
+
+If you see a &quot;No options available&quot; within the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
+
+1. Click on the **pencil** icon adjacent to the dataset in the history
+2. A new menu will appear in the center pane of the interface
+3. Click **Datatype** tab
+4. Set **New Type** to **BAM**
+5. Click **Save**
+
+The medatada will be re-detected and you will be able to see the list of reference sequences in the &quot;**Select references (chromosomes and contigs) you would like to restrict bam to**&quot; drop-down.
+
+    </token>
+
+</macros>
diff -r ad3c355b8249 -r 3bade5114f21 test-data/bam_to_sam_out1.sam
--- a/test-data/bam_to_sam_out1.sam	Wed Mar 04 22:28:17 2015 -0500
+++ b/test-data/bam_to_sam_out1.sam	Tue Oct 13 12:53:40 2015 -0400
@@ -1,3 +1,9 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:101
+@SQ	SN:chr7	LN:404
+@SQ	SN:chr8	LN:202
+@RG	ID:0	SM:Hi,Mom!
+@PG	ID:1	PN:Hey!	VN:2.0
 both_reads_align_clip_marked	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
 both_reads_present_only_first_aligns	89	chr7	1	255	101M	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
 read_2_too_many_gaps	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
diff -r ad3c355b8249 -r 3bade5114f21 test-data/bam_to_sam_out2.sam
--- a/test-data/bam_to_sam_out2.sam	Wed Mar 04 22:28:17 2015 -0500
+++ b/test-data/bam_to_sam_out2.sam	Tue Oct 13 12:53:40 2015 -0400
@@ -1,18 +1,6 @@
-bar:record:4	77	chr1	1	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
-bar:record:6	77	chr1	1	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg2
-bar:record:1	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
-bar:record:3	77	chr1	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg2
-bar:record:1	141	chr1	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
-bar:record:7	77	chr1	20	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg2
-bar:record:8	77	chr1	30	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg2
-bar:record:4	141	chr1	40	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
-bar:record:5	77	chr1	40	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg2
-bar:record:6	141	chr1	50	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg2
-bar:record:2	77	chr2	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
-bar:record:2	141	chr2	30	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg2
-bar:record:3	141	chr3	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
-bar:record:8	141	chr3	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
-bar:record:5	141	chr3	40	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
-bar:record:9	77	chr4	10	0	*	*	0	0	AAAAAAAAAAAAA	1111111111111	RG:Z:rg1
-bar:record:7	141	chr4	20	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
-bar:record:9	141	chr4	60	0	*	*	0	0	CCCCCCCCCCCCC	2222222222222	RG:Z:rg1
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:chr1	LN:101
+@SQ	SN:chr7	LN:404
+@SQ	SN:chr8	LN:202
+@RG	ID:0	SM:Hi,Mom!
+@PG	ID:1	PN:Hey!	VN:2.0
diff -r ad3c355b8249 -r 3bade5114f21 test-data/bam_to_sam_out3.sam
--- a/test-data/bam_to_sam_out3.sam	Wed Mar 04 22:28:17 2015 -0500
+++ b/test-data/bam_to_sam_out3.sam	Tue Oct 13 12:53:40 2015 -0400
@@ -1,9 +1,3 @@
-@HD	VN:1.0	SO:coordinate
-@SQ	SN:chr1	LN:101
-@SQ	SN:chr7	LN:404
-@SQ	SN:chr8	LN:202
-@RG	ID:0	SM:Hi,Mom!
-@PG	ID:1	PN:Hey!	VN:2.0
 both_reads_align_clip_marked	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
 both_reads_present_only_first_aligns	89	chr7	1	255	101M	*	0	0	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
 read_2_too_many_gaps	83	chr7	1	255	101M	=	302	201	CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN	)'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/&	RG:Z:0
diff -r ad3c355b8249 -r 3bade5114f21 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 04 22:28:17 2015 -0500
+++ b/tool_dependencies.xml	Tue Oct 13 12:53:40 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="samtools" version="0.1.19">
-        <repository changeset_revision="786e3000ca58" name="package_samtools_0_1_19" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="samtools" version="1.2">
+        <repository changeset_revision="192f00129358" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>