changeset 0:fec346894871 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flaimapper.xml	Fri Nov 07 09:32:29 2014 -0500
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+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="flaimapper" name="FlaiMapper">
+	<description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
+	<requirements>
+		<requirement type="package" version="1.1.0">flaimapper</requirement>
+	</requirements>
+	<command>
+		flaimapper
+			 -v
+			 -f $output_format
+			 -o $output
+			 -m $mask
+			 -r $fasta
+			#for $alignment in $alignments
+				$alignment
+			#end for
+	</command>
+	
+	<inputs>
+		<param name="alignments" type="data" format="bam,sam" label="Alignment file(s)" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" />
+		
+		<param name="mask" type="data" format="gtf,gff,gtf3" label="small ncRNA Annotation (gtf)" help="" />
+		
+		<param name="output_format" type="select" label="Get">
+			<option value="1">Tabular (1 fragment per column)</option>
+			<option value="2">Tabular  (1 precursor per column)</option>
+			<option value="3">GenBank</option>
+			<!-- option value="gtf">GTF/GFF</option -->
+		</param>
+		
+		<param name="fasta" type="data" format="fa,fasta" label="Fasta sequence corresponding to reference genome" help="" />
+	</inputs>
+	
+	<outputs>
+		<data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
+	</outputs>
+	
+	<help>
+		FlaiMapper: computational annotation of small ncRNA derived fragments using RNA-seq high throughput data
+		
+		doi:10.1093/bioinformatics/btu696
+	</help>
+</tool>
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Fri Nov 07 09:32:29 2014 -0500
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+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+	<!-- Location of all GFF/GTF files -->
+	<table name="gene_sets" comment_char="#">
+		<columns>name, dbkey, value, provider, reference</columns>
+		<file path="tool-data/gene_sets.loc" />
+	</table>
+</tables>
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Nov 07 09:32:29 2014 -0500
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<package name="pysam" version="0.7.7">
+		<repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+	</package>
+	
+	<package name="flaimapper" version="1.1.0">
+		<install version="1.0">
+			<actions>
+				<action type="shell_command">git clone --recursive https://github.com/yhoogstrate/flaimapper.git ; git reset --hard "109a7ee13cfad6eb4746422a5382a928e141d0a1" ; cd flaimapper/src ; python setup.py build </action><!-- 109a7ee13cfad6eb4746422a5382a928e141d0a1 should be the latest 1.1.0 commit -->
+				<action type="make_directory">$INSTALL_DIR/lib/python</action>
+				<action type="make_directory">$INSTALL_DIR/lib64/python</action>
+				<action type="shell_command">export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python &amp;&amp; python setup.py install --home $INSTALL_DIR --install-scripts $INSTALL_DIR/bin</action>
+				
+				<action type="set_environment">
+					<environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
+					<environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+				</action>
+			</actions>
+		</install>
+	</package>
+</tool_dependency>