# HG changeset patch
# User yhoogstrate
# Date 1438335048 14400
# Node ID efd29213e8e5eedb536fd149ab32685cdf6ddc6a
# Parent  affc5ec4f65aab68331e52901475ee360890a3af
Uploaded

diff -r affc5ec4f65a -r efd29213e8e5 flaimapper.xml
--- a/flaimapper.xml	Fri Jul 31 05:07:26 2015 -0400
+++ b/flaimapper.xml	Fri Jul 31 05:30:48 2015 -0400
@@ -1,69 +1,69 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper" name="FlaiMapper" version="1.2.1.w1">
-	<description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
-	<requirements>
-		<requirement type="package" version="1.2.1">flaimapper</requirement>
-	</requirements>
-	
-	<stdio>
-		<regex match="in parse_gff.*?ValueError: invalid literal for int\(\) with base 10" source="stderr" level="fatal" description="The GTF file is corrupt: double check the columns of your GTF/GFF file.\n" />
-		<regex match="[fai_load] build FASTA index." source="stderr" level="log" />
-	</stdio>
-	
-	<version_command>flaimapper --version</version_command>
-	
-	<command>
-		flaimapper
-			 -v
-			 -f $output_format
-			 -o $output
-			 -m $mask
-			 -r $fasta
-		
-		#for $alignment in $alignments
-			$alignment
-		#end for
-	</command>
-	
-	<inputs>
-		<param name="alignments" type="data" format="bam" label="Alignment file(s)" help="Aligned small RNA-Seq reads which may not be fragmented. In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments." multiple="true" />
-		
-		<param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" />
-			
-		<param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
-		
-		<param name="output_format" type="select" label="Output format">
-			<option value="1">Tabular (1 fragment per column)</option>
-			<option value="2">Tabular (1 precursor per column)</option>
-			<option value="3">GenBank</option>
-			<!-- option value="gtf">GTF/GFF</option -->
-		</param>
-	</inputs>
-	
-	<outputs>
-		<data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
-	</outputs>
-	
-	<tests>
-		<test><!-- Testing "ncRNAdb09 alignment"-type analysis -->
-			<param name="alignments"	value="test1/snord81.bam"		ftype="bam" />
-			<param name="mask"			value="test1/ncrnadb09.v2.gtf"	ftype="gtf" />
-			<param name="fasta"			value="test1/ncrnadb09.fa"		ftype="fasta" />
-			<param name="output_format"	value="1" />
-			
-			<output name="output"		file="test1/snord81.flaimapper.txt" />
-		</test>
-		<test><!-- Testing "Full genome alignment"-type analysis -->
-			<param name="alignments"	value="test2/test_genomic_alignment.bam"		ftype="bam" />
-			<param name="mask"			value="test2/test_genomic_genes.gtf"			ftype="gtf" />
-			<param name="fasta"			value="test2/test_genomic_all_chromosomes.fa"	ftype="fasta" />
-			<param name="output_format"	value="1" />
-			
-			<output name="output"		file="test2/test_genomic_flaimapper_output.txt" />
-		</test>
-	</tests>
-	
-	<help>
+<tool id="flaimapper" name="FlaiMapper" version="1.2.1.w2">
+    <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
+    <requirements>
+        <requirement type="package" version="1.2.1">flaimapper</requirement>
+    </requirements>
+    
+    <stdio>
+        <regex match="in parse_gff.*?ValueError: invalid literal for int\(\) with base 10" source="stderr" level="fatal" description="The GTF file is corrupt: double check the columns of your GTF/GFF file.\n" />
+        <regex match="[fai_load] build FASTA index." source="stderr" level="log" />
+    </stdio>
+    
+    <version_command>flaimapper --version</version_command>
+    
+    <command><![CDATA[
+        flaimapper
+             -v
+             -f $output_format
+             -o $output
+             -m $mask
+             -r $fasta
+        
+        #for $alignment in $alignments
+            $alignment
+        #end for
+    ]]></command>
+    
+    <inputs>
+        <param name="alignments" type="data" format="bam" label="Alignment file(s)" help="Aligned small RNA-Seq reads which may not be fragmented. In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments." multiple="true" />
+        
+        <param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" />
+            
+        <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
+        
+        <param name="output_format" type="select" label="Output format">
+            <option value="1">Tabular (1 fragment per column)</option>
+            <option value="2">Tabular (1 precursor per column)</option>
+            <option value="3">GenBank</option>
+            <!-- option value="gtf">GTF/GFF</option -->
+        </param>
+    </inputs>
+    
+    <outputs>
+        <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
+    </outputs>
+    
+    <tests>
+        <test><!-- Testing "ncRNAdb09 alignment"-type analysis -->
+            <param name="alignments"    value="test1/snord81.bam"        ftype="bam" />
+            <param name="mask"            value="test1/ncrnadb09.v2.gtf"    ftype="gtf" />
+            <param name="fasta"            value="test1/ncrnadb09.fa"        ftype="fasta" />
+            <param name="output_format"    value="1" />
+            
+            <output name="output"        file="test1/snord81.flaimapper.txt" />
+        </test>
+        <test><!-- Testing "Full genome alignment"-type analysis -->
+            <param name="alignments"    value="test2/test_genomic_alignment.bam"        ftype="bam" />
+            <param name="mask"            value="test2/test_genomic_genes.gtf"            ftype="gtf" />
+            <param name="fasta"            value="test2/test_genomic_all_chromosomes.fa"    ftype="fasta" />
+            <param name="output_format"    value="1" />
+            
+            <output name="output"        file="test2/test_genomic_flaimapper_output.txt" />
+        </test>
+    </tests>
+    
+    <help><![CDATA[
 FlaiMapper wrapper for Galaxy
 =============================
 
@@ -156,14 +156,13 @@
 * Repository-Maintainer: Youri Hoogstrate
 * Repository-Developers: Youri Hoogstrate
 
-* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
+* Repository-Development: https://github.com/ErasmusMC-Bioinformatics/galaxy-tools
 
 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
 Medical Center (Rotterdam, Netherlands).
-
-	</help>
-	
-	<citations>
-		<citation type="doi">10.1093/bioinformatics/btu696</citation>
-	</citations>
+    ]]></help>
+    
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btu696</citation>
+    </citations>
 </tool>