# HG changeset patch
# User lparsons
# Date 1397243128 14400
# Node ID 227f9d3f0e323f259f67e828e023c3c4e0bde5b4
# Parent  3ffe4e2572a742b9573f5cec44ac3b412e1de8a6
Updated HTSeq package to version 0.6.1, fixed input format string, updated dependency definitions

diff -r 3ffe4e2572a7 -r 227f9d3f0e32 .hgignore
--- a/.hgignore	Mon Jan 27 14:12:46 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-^package$
-syntax: glob
-*.pyc
diff -r 3ffe4e2572a7 -r 227f9d3f0e32 .hgtags
--- a/.hgtags	Mon Jan 27 14:12:46 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-142ec9462fa644cd29642ea0ad10e9889ce75619 0.3
-3e7b1e8a69f9d79b8de603f24e466deb7b192100 0.3.release2
-496a7dc0786f8367264520dfff6e8e8e744de3b2 0.3.1
diff -r 3ffe4e2572a7 -r 227f9d3f0e32 README.md
--- a/README.md	Mon Jan 27 14:12:46 2014 -0500
+++ b/README.md	Fri Apr 11 15:05:28 2014 -0400
@@ -9,7 +9,7 @@
 Installation
 ------------
 
-Installtion directly from the [Galaxy
+Installation directly from the [Galaxy
 Toolshed](http://toolshed.g2.bx.psu.edu/view/lparsons/htseq_count) is
 recommended.
 
@@ -24,7 +24,7 @@
 License
 -------
 
-Copyright (c) 2012-2013, Lance R. Parsons <lparsons@princeton.edu>  
+Copyright (c) 2012-2014, Lance R. Parsons <lparsons@princeton.edu>  
 All rights reserved.
 
 Licensed under the BSD 2-Clause License: <http://opensource.org/licenses/BSD-2-Clause>
diff -r 3ffe4e2572a7 -r 227f9d3f0e32 fabfile.py
--- a/fabfile.py	Mon Jan 27 14:12:46 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-from fabric.api import local
-from fabric.operations import prompt
-import os
-
-
-def package():
-    '''
-    Pacakge for upload to toolshed
-      packaging 'test' version (default) uses local directory
-      otherwise, specify a mercurial tag to package
-    '''
-    package_dir = 'package'
-    base_filename = os.path.join(package_dir, 'htseq-count')
-    version = prompt("Enter version number for package [test]:")
-    revision_option = ''
-    if version != '':
-        revision_option = '-r "%s"' % version
-    else:
-        version = 'test'
-    version_filename = '%s_%s.tar.gz' % (base_filename, version)
-    local('mkdir -p %s' % package_dir)
-    local('rm -f %s' % version_filename)
-    if version == 'test':
-        local('tar czvf %s --exclude "fabfile.*" --exclude "%s" --exclude ".hg*" *' % (version_filename, package_dir))
-    else:
-        local('hg archive -t tgz %s -X "fabfile.*" -X "package" -X ".hg*" -p . "%s"' % (revision_option, version_filename))
diff -r 3ffe4e2572a7 -r 227f9d3f0e32 htseq-count.xml
--- a/htseq-count.xml	Mon Jan 27 14:12:46 2014 -0500
+++ b/htseq-count.xml	Fri Apr 11 15:05:28 2014 -0400
@@ -1,11 +1,10 @@
-<tool id="htseq_count" name="htseq-count" version="0.3.2">
+<tool id="htseq_count" name="htseq-count" version="0.4">
     <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>
     <version_command>htseq-count -h | grep version | sed 's/^\(.*\)*\(version .*\)\./\2/'</version_command>
     <requirements>
         <requirement type="package" version="1.7.1">numpy</requirement>
-        <requirement type="package" version="0.5.4p5">htseq</requirement>
+        <requirement type="package" version="0.6.1">htseq</requirement>
         <requirement type="package" version="0.1.19">samtools</requirement>
-        <requirement type="package" version="1.56.0">picard</requirement> 
     </requirements>
     <command>
     ##set up input files
@@ -18,18 +17,9 @@
             #set $reference_fasta_filename = str( $samout_conditional.reference_source.ref_file.fields.path )
         #end if
     #end if
-    #if str($singlepaired) == "paired":
-        ln -s $samfile local_input.sam &amp;&amp;
-        java -Xmx2G -jar "\$JAVA_JAR_PATH/SortSam.jar" VALIDATION_STRINGENCY=LENIENT SORT_ORDER=queryname O=prepared_input.sam I=local_input.sam TMP_DIR="${__new_file_path__}" 
-        || echo "Error running Picard MergeSamFiles" &gt;&amp;2 &amp;&amp;
-    #else:
-        #if $samfile.extension == "bam":
-            samtools view $samfile | 
-        #else
-            ln -s $samfile prepared_input.sam &amp;&amp;
-        #end if
-    #end if
     htseq-count 
+    --format=$samfile.extension
+    --order=pos
     --mode=$mode 
     --stranded=$stranded 
     --minaqual=$minaqual 
@@ -38,27 +28,14 @@
     #if $samout_conditional.samout:
         --samout=$__new_file_path__/${samoutfile.id}_tmp
     #end if
-    #if str($singlepaired) == "paired":
-        prepared_input.sam
-    #else:
-        #if $samfile.extension == "bam":
-            - 
-        #else:
-            prepared_input.sam
-        #end if
-    #end if    
+    $samfile
     $gfffile 
     | awk '{if ($1 ~ "no_feature|ambiguous|too_low_aQual|not_aligned|alignment_not_unique") print $0 | "cat 1>&amp;2"; else print $0}' &gt; $counts 2&gt;$othercounts
     #if $samout_conditional.samout:
         &amp;&amp; samtools view -Su -t ${reference_fasta_filename}.fai $__new_file_path__/${samoutfile.id}_tmp | samtools sort -o - sorted > $samoutfile
     #end if</command>
     <inputs>
-        <param format="sam, bam" name="samfile" type="data" label="Aligned SAM/BAM File"/>
-        <param name="singlepaired" type="select" label="Is this library mate-paired?">
-            <help>Paired libraries will be sorted by read name prior to counting.</help>
-            <option value="single" selected="true">single-end</option>
-            <option value="paired">paired-end</option>
-        </param>
+        <param format="sam,bam" name="samfile" type="data" label="Aligned SAM/BAM File"/>
         <param format="gff" name="gfffile" type="data" label="GFF File"/>
         <param name="mode" type="select" label="Mode">
             <help>Mode to handle reads overlapping more than one feature.</help>
@@ -72,7 +49,7 @@
             <option value="no">No</option>
             <option value="reverse">Reverse</option>
         </param>
-        <param name="minaqual" type="integer" value="0" label="Minimum alignment quality">
+        <param name="minaqual" type="integer" value="10" label="Minimum alignment quality">
             <help>Skip all reads with alignment quality lower than the given minimum value</help>
         </param>
         <param name="featuretype" type="text" value="exon" label="Feature type">
@@ -188,8 +165,7 @@
 
 The following figure illustrates the effect of these three modes:
 
-.. image:: $PATH_TO_IMAGES/count_modes.png
-    :width: 500
+.. image:: count_modes.png
 
 
 Strandedness
diff -r 3ffe4e2572a7 -r 227f9d3f0e32 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Jan 27 14:12:46 2014 -0500
+++ b/tool_dependencies.xml	Fri Apr 11 15:05:28 2014 -0400
@@ -2,24 +2,20 @@
 <tool_dependency>
 
     <package name="numpy" version="1.7.1">
-        <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
 
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-
-    <package name="picard" version="1.56.0">
-        <repository changeset_revision="61e41d21cb6f" name="package_picard_1_56_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
 
-    <package name="htseq" version="0.5.4p5">
+    <package name="htseq" version="0.6.1">
         <install version="1.0">
             <actions>
-                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.4p5.tar.gz</action>
+                <action type="download_by_url">https://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.6.1.tar.gz</action>
                 <!-- populate the environment variables from the dependend repos -->
                 <action type="set_environment_for_install">
-                    <repository changeset_revision="028df1ddd7a2" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="0c288abd2a1e" name="package_numpy_1_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu">
                         <package name="numpy" version="1.7.1" />
                    </repository>
                 </action>