# HG changeset patch
# User yhoogstrate
# Date 1438335170 14400
# Node ID 3074e91f9f80685ce1098119409e6f830deda7b8
# Parent  abbfa4c2e35671871c536b8a85bd708750d2fe4c
Uploaded

diff -r abbfa4c2e356 -r 3074e91f9f80 flaimapper.xml
--- a/flaimapper.xml	Fri Jul 31 05:09:32 2015 -0400
+++ b/flaimapper.xml	Fri Jul 31 05:32:50 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>