diff flaimapper.xml @ 8:4f22bd612754 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad

--- a/flaimapper.xml	Fri Apr 28 07:05:48 2017 -0400
+++ b/flaimapper.xml	Wed Aug 16 11:07:51 2017 -0400
@@ -1,12 +1,12 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="flaimapper" name="FlaiMapper" version="2.4.0-0">
+<tool id="flaimapper" name="FlaiMapper" version="2.5.0-0">
     <description>detects small ncRNA derived fragments in small RNA-Seq data</description>
     <requirements>
-        <requirement type="package" version="2.4.0">flaimapper</requirement>
+        <requirement type="package" version="2.5.0">flaimapper</requirement>
     </requirements>
-    
-    <version_command>flaimapper --version 2&gt;&amp;1 | head -n 1</version_command>
-    
+
+    <version_command><![CDATA[ flaimapper --version 2>&1 | head -n 1 ]]></version_command>
+
     <command detect_errors="exit_code"><![CDATA[
         flaimapper
             -v
@@ -28,24 +28,24 @@
 
             '${alignment}'
     ]]></command>
-    
+
     <inputs>
         <param name="alignment" type="data" format="bam" multiple="false"
                label="Alignment file"
                help="Aligned small RNA-Seq reads must be single end and should not be fragmented in the library preparation" />
-        
+
         <conditional name="output_select">
             <param name="output_format" type="select" label="Output format" argument="-f">
                 <option value="1">Tabular</option>
                 <option value="2">GTF</option>
             </param>
-            
+
             <when value="1">
                 <param name="fasta" type="data" format="fasta" optional="true"
                        label="(Optional) Genome reference in FASTA format that corresponds to the reference genome or RNA database"
                        help="By selecting this file, sequences will be provided in the corresponding column in the output file" argument="-r" />
             </when>
-            
+
             <when value="2">
                 <param name="offset5p" type="integer" value="4"
                        label="Add 5'-offset to exon-type entry in GTF output file"
@@ -55,12 +55,12 @@
                        help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to add an offset to allow less stringent read counting." argument="--offset3p" />
             </when>
         </conditional>
-        
+
         <param name="parameters" type="data" format="txt,tabular" optional="true"
                label="(Optional) Custom parameters file" help="" argument="-p" />
-        
+
     </inputs>
-    
+
     <outputs>
         <data format="tabular" name="output"
               label="${tool.name} on $on_string">
@@ -70,68 +70,72 @@
             </change_format>
         </data>
     </outputs>
-    
+
     <tests>
         <!-- tabular -->
-        <test><!-- Testing "ncRNAdb09 alignment"-type analysis -->
+        <!-- Testing "ncRNAdb09 alignment"-type analysis -->
+        <test>
             <param name="alignment" value="snord81.bam" ftype="bam" />
             <param name="fasta" value="snord81.fa" ftype="fasta" />
             <param name="output_format" value="1" />
-            
+
             <output name="output" file="snord81.flaimapper.txt" />
         </test>
         <test>
             <param name="alignment" value="snord81.bam" ftype="bam" />
             <param name="output_format" value="1" />
-            
+
             <output name="output" file="snord81.flaimapper.no-seq.txt" />
         </test>
-        <test><!-- Testing "Full genome alignment"-type analysis -->
+        <!-- Testing "Full genome alignment"-type analysis -->
+        <test>
             <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
             <param name="fasta" value="test_genomic_all_chromosomes.fa" ftype="fasta" />
             <param name="output_format" value="1" />
-            
+
             <output name="output" file="test_genomic_flaimapper_output.txt" />
         </test>
         <test>
             <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
             <param name="output_format" value="1" />
-            
+
             <output name="output" file="test_genomic_flaimapper_output.no-seq.txt" />
         </test>
-        
+
         <!-- GTF -->
-        <test><!-- Testing "ncRNAdb09 alignment"-type analysis -->
+        <!-- Testing "ncRNAdb09 alignment"-type analysis -->
+        <test>
             <param name="alignment" value="snord81.bam" ftype="bam" />
             <param name="output_format" value="2" />
-            
+
             <output name="output" file="snord81.flaimapper.gtf" />
         </test>
-        <test><!-- Testing "Full genome alignment"-type analysis -->
+        <!-- Testing "Full genome alignment"-type analysis -->
+        <test>
             <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
             <param name="output_format" value="2" />
-            
+
             <output name="output" file="test_genomic_flaimapper_output.gtf" />
         </test>
-        
+
         <!-- test custom parameters -->
         <test>
             <param name="alignment" value="snord81.bam" ftype="bam" />
             <param name="output_format" value="2" />
             <param name="offset5p" value="5" />
             <param name="offset3p" value="5" />
-            
+
             <output name="output" file="snord81.flaimapper.offsets_5_5.gtf" />
         </test>
         <test>
             <param name="alignment" value="snord81.bam" ftype="bam" />
             <param name="output_format" value="2" />
             <param name="parameters" value="filter-parameters.duck.15.txt"/>
-            
+
             <output name="output" file="snord81.flaimapper.duck-15.gtf" />
         </test>
     </tests>
-    
+
     <help><![CDATA[
 FlaiMapper wrapper for Galaxy
 =============================
@@ -171,8 +175,8 @@
 
 https://github.com/yhoogstrate/flaimapper
     ]]></help>
-    
+
     <citations>
         <citation type="doi">10.1093/bioinformatics/btu696</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>