# HG changeset patch
# User Lance Parsons <lparsons@princeton.edu>
# Date 1347312610 14400
# Node ID f7a5b54a8d4f84c199fc1fc1fd1eb86f9bbc4ed6
# Parent  f5d08224af89bfbe0b6dc7ce190a74f55eab890b
Split feature and non-feature counts, removed tool_dependencies.xml (for now)

diff -r f5d08224af89 -r f7a5b54a8d4f htseq-count.xml
--- a/htseq-count.xml	Tue Sep 04 14:16:33 2012 -0400
+++ b/htseq-count.xml	Mon Sep 10 17:30:10 2012 -0400
@@ -1,4 +1,4 @@
-<tool id="htseq_count" name="htseq-count" version="0.1">
+<tool id="htseq_count" name="htseq-count" version="0.2">
     <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>
@@ -35,7 +35,7 @@
         $samfile 
     #end if
     $gfffile 
-    &gt; $counts
+    | 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>
@@ -93,6 +93,7 @@
 
     <outputs>
         <data format="tabular" name="counts" label="${tool.name} on ${on_string}"/>
+        <data format="tabular" name="othercounts" label="${tool.name} on ${on_string} (no feature)"/>
         <data format="bam" name="samoutfile" label="${tool.name} on ${on_string} (BAM)">
             <filter>samout_conditional['samout']</filter>
         </data>
@@ -108,12 +109,14 @@
             <param name="gfffile" value="htseq-test.gff" />
             <param name="samout" value="False" />
             <output name="counts" file="htseq-test_counts.tsv" />
+            <output name="othercounts" file="htseq-test_othercounts.tsv" />
         </test>
         <test>
             <param name="samfile" value="htseq-test.bam" />
             <param name="gfffile" value="htseq-test.gff" />
             <param name="samout" value="False" />
             <output name="counts" file="htseq-test_counts.tsv" />
+            <output name="othercounts" file="htseq-test_othercounts.tsv" />
         </test>
         <!-- Seems to be an issue setting the $reference_fasta_filename variable during test
         <test>
@@ -123,6 +126,7 @@
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" value="htseq-test_reference.fasta" />
             <output name="counts" file="htseq-test_counts.tsv" />
+            <output name="othercounts" file="htseq-test_othercounts.tsv" />
             <output name="samoutfile" file="htseq-test_samout.bam" />
         </test>
         -->
diff -r f5d08224af89 -r f7a5b54a8d4f test-data/htseq-test_counts.tsv
--- a/test-data/htseq-test_counts.tsv	Tue Sep 04 14:16:33 2012 -0400
+++ b/test-data/htseq-test_counts.tsv	Mon Sep 10 17:30:10 2012 -0400
@@ -7122,8 +7122,3 @@
 tY(GUA)M2	0
 tY(GUA)O	0
 tY(GUA)Q	0
-no_feature	1437
-ambiguous	67
-too_low_aQual	0
-not_aligned	1336
-alignment_not_unique	0
diff -r f5d08224af89 -r f7a5b54a8d4f test-data/htseq-test_othercounts.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/htseq-test_othercounts.tsv	Mon Sep 10 17:30:10 2012 -0400
@@ -0,0 +1,5 @@
+no_feature	1437
+ambiguous	67
+too_low_aQual	0
+not_aligned	1336
+alignment_not_unique	0
diff -r f5d08224af89 -r f7a5b54a8d4f tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Sep 04 14:16:33 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="htseq" version="0.5.3p9">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://pypi.python.org/packages/source/H/HTSeq/HTSeq-0.5.3p9.tar.gz</action>
-                <action type="shell_command">mkdir -p $INSTALL_DIR/lib/python</action>
-                <action type="set_environment">
-                    <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
-                </action>
-                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py build</action>
-                <action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            Installation of HTSeq requires Python 2.5+ (does not yet work with Python 3), and the Nympy Python package.
-        </readme>
-    </package>
-    <package name="samtools" version="0.1.18">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2</action>
-                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/g' Makefile</action>
-                <action type="shell_command">make</action>
-                <action type="move_file">
-                    <source>samtools</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>misc/maq2sam-long</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            Compiling SAMtools requires the ncurses and zlib development libraries.
-        </readme>
-    </package>
-</tool_dependency>