# HG changeset patch
# User fubar
# Date 1375926841 14400
# Node ID 3906fe90d881c8ad263d5cbe0ad16afbf801d13a
# Parent  6ccbf28d0a078917b3bca39b94e6d812d00f233e
Uploaded

diff -r 6ccbf28d0a07 -r 3906fe90d881 htseq_bams_to_count_matrix/generatetest.sh
--- a/htseq_bams_to_count_matrix/generatetest.sh	Sat Jun 15 20:00:58 2013 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-python ../htseqsams2mx.py -g rn4_chr20_100k.gtf -o test.xls --samf "'rn4chr20test1.bam','col1'" --samf "'rn4chr20test2.bam','col2'"
diff -r 6ccbf28d0a07 -r 3906fe90d881 htseq_bams_to_count_matrix/htseqsams2mx.xml
--- a/htseq_bams_to_count_matrix/htseqsams2mx.xml	Sat Jun 15 20:00:58 2013 -0400
+++ b/htseq_bams_to_count_matrix/htseqsams2mx.xml	Wed Aug 07 21:54:01 2013 -0400
@@ -1,4 +1,4 @@
-<tool id="htseqsams2mx" name="SAM/BAM to count matrix" version="0.2">
+<tool id="htseqsams2mx" name="SAM/BAM to count matrix" version="0.3">
  <description>using HTSeq code</description>
   <stdio>
      <exit_code range="666"   level="warning"   
@@ -6,6 +6,7 @@
   </stdio>
   <requirements>
       <requirement type="package" version="1.7.1">numpy</requirement>
+      <requirement type="package" version="0.7.5">pysam</requirement>
       <requirement type="package" version="2.4.11">freetype</requirement>
       <requirement type="package" version="1.2.1">matplotliblite</requirement> 
       <requirement type="package" version="0.5.4p3">htseq</requirement>
diff -r 6ccbf28d0a07 -r 3906fe90d881 htseq_bams_to_count_matrix/tool_dependencies.xml
--- a/htseq_bams_to_count_matrix/tool_dependencies.xml	Sat Jun 15 20:00:58 2013 -0400
+++ b/htseq_bams_to_count_matrix/tool_dependencies.xml	Wed Aug 07 21:54:01 2013 -0400
@@ -3,6 +3,9 @@
     <package name="numpy" version="1.7.1">
         <repository changeset_revision="af9633757cf0" name="package_numpy_1_7" owner="blankenberg" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
+    <package name="pysam" version="0.7.5">
+        <repository changeset_revision="a4e35f23093f" name="package_pysam_0_7_5" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
     <package name="freetype" version="2.4.11">
         <repository changeset_revision="4e54e357ac25" name="package_freetype_2_4" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
     </package>
@@ -19,6 +22,9 @@
                         <repository changeset_revision="af9633757cf0" name="package_numpy_1_7" owner="blankenberg" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
                             <package name="numpy" version="1.7.1" />
                         </repository>
+                        <repository changeset_revision="a4e35f23093f" name="package_pysam_0_7_5" owner="fubar" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                            <package name="pysam" version="0.7.5" />
+                        </repository>
                         <repository changeset_revision="4e54e357ac25" name="package_freetype_2_4" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/">
                             <package name="freetype" version="2.4.11" />
                         </repository>
@@ -34,7 +40,7 @@
             </actions>
         </install>
         <readme>
-            Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Numpy Python package. 
+            Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), pysam and the Numpy Python package. 
             Note this uses the matplotlib lite version dependent on the lite version of numpy - no atlas compilation 
         </readme>
     </package>