# HG changeset patch
# User yhoogstrate
# Date 1438695809 14400
# Node ID 9750f8c1d3cbe60ce371df2788bbae7f713c260b
# Parent  cb854f5d6a4ba214c8a392491f944c26e05da957
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a-dirty

diff -r cb854f5d6a4b -r 9750f8c1d3cb crossmap.xml
--- a/crossmap.xml	Tue Aug 04 08:57:24 2015 -0400
+++ b/crossmap.xml	Tue Aug 04 09:43:29 2015 -0400
@@ -5,7 +5,10 @@
         <requirement type="package" version="0.1.9">crossmap</requirement>
     </requirements>
     
-    <stdio></stdio>
+    <stdio>
+        <regex match="Usage: CrossMap.py" source="stdin" level="fatal"/>
+        <regex match="^@ " source="stdin" level="warning" />
+    </stdio>
 
     <command>
         CrossMap.py
@@ -18,11 +21,13 @@
                 "$multiple.seq_source.input_chain"
             #end if
             
+<!-- these arguments don't work
             #if $multiple.input_format == "bam"
                 -m $multiple.insert_size
                 -s $multiple.insert_size_stdev
                 -t $multiple.insert_size_fold
             #end if
+-->
             
             "$multiple.seq_source.input"
             
@@ -69,9 +74,11 @@
                         </when>
                 </conditional>
                 
+<!-- These parameters don't work
                 <param name="insert_size" type="float" value="200.0" label="Insert size (-m)" help="Average insert size of pair-end sequencing (bp) [default=200.0]" />
                 <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev (-s)" help="Stanadard deviation of insert size. [default=30.0]" />
                 <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange (-t)" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]" />
+-->
             </when>
             <when value="bed">
                 <conditional name="seq_source">
@@ -236,13 +243,13 @@
     </inputs>
     
     <outputs>
-        <data format="text" name="output" label="Output file">
-        </data>
+        <data format="text" name="output" label="${tool.name} on ${input.hid}: ${input.name}" />
     </outputs>
     
     <tests>
         <test>
             <param name="input" value="test1.hg19.txt"/>
+            <param name="input" value="hg18tohg19.chain"/>
             <output name="output" file="test1.hg18.txt"/>
         </test>
     </tests>
@@ -252,6 +259,12 @@
 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
 GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
 and VCF, reading from remote servers and file compression are supported.
+
+CrossMap bed
+------------
+BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
+BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
+
     </help>
     
     <citations>