# HG changeset patch
# User yhoogstrate
# Date 1426774666 14400
# Node ID c5df479c423bf3dd001b236ec5998c65b3ccb144
# Parent  548e7c482077dd4ff377cb0fd50e61bf688b7528
Uploaded

diff -r 548e7c482077 -r c5df479c423b README.md
diff -r 548e7c482077 -r c5df479c423b egg/flaimapper-1.1.2-py2.7.egg
Binary file egg/flaimapper-1.1.2-py2.7.egg has changed
diff -r 548e7c482077 -r c5df479c423b flaimapper.xml
--- a/flaimapper.xml	Fri Nov 07 10:54:58 2014 -0500
+++ b/flaimapper.xml	Thu Mar 19 10:17:46 2015 -0400
@@ -1,39 +1,39 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper" name="FlaiMapper" version="1.1.0">
+<tool id="flaimapper" name="FlaiMapper" version="1.1.2.a">
 	<description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
 	<requirements>
-		<requirement type="package" version="1.1.0">flaimapper</requirement>
 		<requirement type="package" version="0.7.7">pysam</requirement>
+		<requirement type="package" version="0.8.1">pysam</requirement>
+		<requirement type="package" version="1.1.2">flaimapper</requirement>
 	</requirements>
+	
+	<version_command>flaimapper --version</version_command>
+	
 	<command>
-		##rm $mask".tbi"
-		##rm $fasta".fai"
-		
 		flaimapper
 			 -v
 			 -f $output_format
 			 -o $output
 			 -m $mask
 			 -r $fasta
-			#for $alignment in $alignments
-				$alignment
-			#end for
+		
+		#for $alignment in $alignments
+			$alignment
+		#end for
 	</command>
 	
-	<version_command>flaimapper --version</version_command>
-	
 	<inputs>
 		<param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" />
 		
 		<param name="mask" type="data" format="gtf,gff,gtf3" label="small ncRNA Annotation (gtf)" help="" />
-		
+			
 		<param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
 		
 		<param name="output_format" type="select" label="Output format">
-			<option value="1">Tabular (1 fragment per column)</option>
-			<option value="2">Tabular  (1 precursor per column)</option>
-			<option value="3">GenBank</option>
-			<!-- option value="gtf">GTF/GFF</option -->
+		<option value="1">Tabular (1 fragment per column)</option>
+		<option value="2">Tabular (1 precursor per column)</option>
+		<option value="3">GenBank</option>
+		<!-- option value="gtf">GTF/GFF</option -->
 		</param>
 	</inputs>
 	
@@ -42,6 +42,8 @@
 	</outputs>
 	
 	<help>
+		You must have 'easy_install' installed.
+		
 		FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data
 		
 		doi:10.1093/bioinformatics/btu696
diff -r 548e7c482077 -r c5df479c423b tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Fri Nov 07 10:54:58 2014 -0500
+++ b/tool_data_table_conf.xml.sample	Thu Mar 19 10:17:46 2015 -0400
@@ -1,8 +1,8 @@
 <!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
 <tables>
-	<!-- Location of all GFF/GTF files -->
-	<table name="gene_sets" comment_char="#">
-		<columns>name, dbkey, value, provider, reference</columns>
-		<file path="tool-data/gene_sets.loc" />
-	</table>
+<!-- Location of all GFF/GTF files -->
+<table name="gene_sets" comment_char="#">
+<columns>name, dbkey, value, provider, reference</columns>
+<file path="tool-data/gene_sets.loc" />
+</table>
 </tables>
\ No newline at end of file
diff -r 548e7c482077 -r c5df479c423b tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Nov 07 10:54:58 2014 -0500
+++ b/tool_dependencies.xml	Thu Mar 19 10:17:46 2015 -0400
@@ -1,19 +1,33 @@
 <?xml version="1.0"?>
 <tool_dependency>
 	<package name="pysam" version="0.7.7">
-		<repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+		<repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 	</package>
 	
-	<package name="flaimapper" version="1.1.0">
+	<package name="pysam" version="0.8.1">
+		<repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+	</package>
+	
+	<package name="flaimapper" version="1.1.2">
 		<install version="1.0">
 			<actions>
-				<action type="shell_command">git clone --quiet --recursive https://github.com/yhoogstrate/flaimapper.git ; cd flaimapper ; git reset --hard "109a7ee13cfad6eb4746422a5382a928e141d0a1" ; cd src ; python setup.py build</action><!-- 109a7ee13cfad6eb4746422a5382a928e141d0a1 should be the latest 1.1.0 commit -->
-				<action type="make_directory">$INSTALL_DIR/lib/python</action>
-				<action type="make_directory">$INSTALL_DIR/lib64/python</action>
-				<action type="shell_command">cd src ; pwd ; ls ; export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
+				
+				<action type="set_environment_for_install">
+					<repository changeset_revision="ca10c522f37e" name="package_pysam_0_7_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+						<package name="pysam" version="0.7.7" />
+					</repository>
+					<repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+						<package name="pysam" version="0.8.1" />
+					</repository>
+				</action>
+				
+				<action type="make_directory">$INSTALL_DIR</action>
+				<action type="make_directory">$INSTALL_DIR/bin</action>
+				
+				<action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR:$INSTALL_DIR"/lib/python":$INSTALL_DIR"/lib64/python":$PYSAM_PATH:$PYSAM_PATH"/lib/python":$PYSAM_PATH"/lib64/python" ; easy_install --prefix=$INSTALL_DIR --install-dir=$INSTALL_DIR --script-dir=$INSTALL_DIR/bin $REPOSITORY_INSTALL_DIR"/egg/flaimapper-1.1.2-py2.7.egg"</action>
 				
 				<action type="set_environment">
-					<environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
+					<environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
 					<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
 				</action>
 			</actions>