diff flaimapper.xml @ 28:19d1402611ef draft

planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty

--- a/flaimapper.xml	Sun Mar 29 05:32:04 2015 -0400
+++ b/flaimapper.xml	Wed Jun 03 07:27:47 2015 -0400
@@ -1,11 +1,15 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper" name="FlaiMapper" version="1.1.5.a">
+<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="0.8.2.1">pysam</requirement>
-		<requirement type="package" version="1.1.5">flaimapper</requirement>
+		<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>
@@ -21,10 +25,6 @@
 		#end for
 	</command>
 	
-	<stdio>
-		<regex match="[fai_load] build FASTA index." source="stderr" level="log" />
-	</stdio>
-	
 	<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" />
 		
@@ -45,13 +45,21 @@
 	</outputs>
 	
 	<tests>
-		<test>
-			<param name="alignments" value="snord81.bam" ftype="bam" />
-			<param name="mask" value="ncrnadb09.gtf" ftype="gtf" />
-			<param name="fasta" value="ncrnadb09.fa" ftype="fasta" />
-			<param name="output_format" value="1" />
+		<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="snord81.flaimapper.txt" />
+			<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>