# HG changeset patch
# User yhoogstrate
# Date 1426862721 14400
# Node ID 0e9520cf7587c594d514d4c287455761880ebbb0
# Parent  be98a7b6c94e769e56e536255980374cc1e4dd62
Uploaded

diff -r be98a7b6c94e -r 0e9520cf7587 README.rst
--- a/README.rst	Fri Mar 20 06:33:35 2015 -0400
+++ b/README.rst	Fri Mar 20 10:45:21 2015 -0400
@@ -0,0 +1,41 @@
+FlaiMapper wrapper for Galaxy
+=============================
+
+https://github.com/yhoogstrate/flaimapper
+http://www.ncbi.nlm.nih.gov/pubmed/25338717
+http://dx.doi.org/10.1093/bioinformatics/btu696
+
+Fragment Location Annotation Identification Mapper
+
+FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
+
+Development
+-----------
+
+* Repository-Maintainer: Youri Hoogstrate
+* Repository-Developers: Youri Hoogstrate
+
+* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
+
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands).
+
+License
+-------
+
+**flaimapper** and **wrapper**:
+
+GPL (>=3)
+
+**pysam**:
+
+The MIT License (>=3)
+
+References
+----------
+**FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.**
+
+*Youri Hoogstrate, Guido Jenster, and Elena S. Martens-Uzunova* - Bioinformatics (2015) 31 (5): 665-673
+
+- http://www.ncbi.nlm.nih.gov/pubmed/25338717
+- http://dx.doi.org/10.1093/bioinformatics/btu696
\ No newline at end of file
diff -r be98a7b6c94e -r 0e9520cf7587 egg/flaimapper-1.1.2-py2.7.egg
Binary file egg/flaimapper-1.1.2-py2.7.egg has changed
diff -r be98a7b6c94e -r 0e9520cf7587 egg/flaimapper-1.1.4-py2.7.egg
Binary file egg/flaimapper-1.1.4-py2.7.egg has changed
diff -r be98a7b6c94e -r 0e9520cf7587 flaimapper.xml
--- a/flaimapper.xml	Fri Mar 20 06:33:35 2015 -0400
+++ b/flaimapper.xml	Fri Mar 20 10:45:21 2015 -0400
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper" name="FlaiMapper" version="1.1.2.d">
+<tool id="flaimapper" name="FlaiMapper" version="1.1.4.a">
 	<description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
 	<requirements>
 		<requirement type="package" version="0.8.2.1">pysam</requirement><!-- pysam 0.7.7 ABSOLUTELY CRASHES !!! -->
-		<requirement type="package" version="1.1.2">flaimapper</requirement>
+		<requirement type="package" version="1.1.4">flaimapper</requirement>
 	</requirements>
 	
 	<version_command>flaimapper --version</version_command>
@@ -19,18 +19,12 @@
 		#for $alignment in $alignments
 			$alignment
 		#end for
-		
-		2&gt; stderr.txt ; 
-		
-		grep -v '[fai_load] build FASTA index.' stderr.txt > stderr2.txt ; rm stderr.txt ; mv stderr2.txt stderr.txt ; 
-		
-		cat stderr.txt >&amp;2
 	</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="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" />
 			
 		<param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
 		
diff -r be98a7b6c94e -r 0e9520cf7587 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Mar 20 06:33:35 2015 -0400
+++ b/tool_dependencies.xml	Fri Mar 20 10:45:21 2015 -0400
@@ -4,7 +4,7 @@
 		<repository changeset_revision="e6c1f548397a" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 	</package>
 	
-	<package name="flaimapper" version="1.1.2">
+	<package name="flaimapper" version="1.1.4">
 		<install version="1.0">
 			<actions>
 				
@@ -17,7 +17,7 @@
 				<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 $REPOSITORY_INSTALL_DIR"/egg/flaimapper-1.1.2-py2.7.egg"</action>
+				<action type="shell_command">export PYTHONPATH=$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-1.1.4-py2.7.egg"</action>
 				
 				<action type="set_environment">
 					<environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>