# HG changeset patch
# User yhoogstrate
# Date 1439475559 14400
# Node ID 263581d4dd90ace74cfde95234cd45bfb6ecca5a
# Parent  22a09104afcc60ac8aa584437f322157cf38aeec
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 74570ff45544cfe08ef65d0b712f8d44da6f545c

diff -r 22a09104afcc -r 263581d4dd90 crossmap.xml
--- a/crossmap.xml	Thu Aug 13 07:52:11 2015 -0400
+++ b/crossmap.xml	Thu Aug 13 10:19:19 2015 -0400
@@ -2,16 +2,17 @@
     <description>Convert genome coordinates or annotation files between genome assemblies</description>
     
     <requirements>
+        <requirement type="package" version="312">ucsc_tools</requirement>
         <requirement type="package" version="0.2">crossmap</requirement>
     </requirements>
     
-    <version_command>CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
-    
     <stdio>
         <regex match="Usage: CrossMap.py" source="stdout" level="fatal"/>
         <regex match=".*" source="both" level="log"/>
     </stdio>
-
+    
+    <version_command>CrossMap.py 2&gt;&amp;1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command>
+    
     <command>
         CrossMap.py
             ${multiple.input_format.replace("sam","bam")}
@@ -47,6 +48,9 @@
             #else if $multiple.input_format in ["vcf"]
                 ; mv "${output}" "$output"
                 ; mv "${output}.unmap" "$output_unmapped"
+            #else if $multiple.input_format in ["wig", "bigwig"]
+                ; mv "${output}.bw" "$output"
+                ; mv "${output}.sorted.bgr" "$output2"
             #end if
     </command>
 
@@ -178,6 +182,8 @@
                             <param type="data" format="csv"    name="input_chain" label="LiftOver chain file" />
                         </when>
                 </conditional>
+                
+                <param name="include_fails" type="hidden" tvalue="False" />
             </when>
             <when value="gff">
                 <conditional name="seq_source">
@@ -290,6 +296,8 @@
                         <param type="data" format="csv" name="input_chain" label="LiftOver chain file" />
                     </when>
                 </conditional>
+                
+                <param name="include_fails" type="hidden" tvalue="False" />
             </when>
         </conditional>
     </inputs>
@@ -303,7 +311,7 @@
                 <when input="multiple.input_format" value="bigwig" format="bigwig" />
                 <when input="multiple.input_format" value="gff" format="gff" />
                 <when input="multiple.input_format" value="vcf" format="vcf" />
-                <when input="imultiple.nput_format" value="wig" format="wig" />
+                <when input="imultiple.nput_format" value="wig" format="bigwig" />
             </change_format>
         </data>
         
@@ -311,11 +319,13 @@
             <filter>input_format in ["bam" , "vcf"]</filter>
             <change_format>
                 <when input="multiple.input_format" value="bam" format="bam" />
-                <when input="multiple.input_format" value="sam" format="sam" />
-                <when input="multiple.input_format" value="bigwig" format="bigwig" />
-                <when input="multiple.input_format" value="gff" format="gff" />
                 <when input="multiple.input_format" value="vcf" format="vcf" />
-                <when input="multiple.input_format" value="wig" format="wig" />
+            </change_format>
+        </data>
+        <data format="text" name="output2" label="${tool.name} on ">
+            <filter>input_format in ["wig"]</filter>
+            <change_format>
+                <when input="multiple.input_format" value="wig" format="bedgraph" />
             </change_format>
         </data>
     </outputs>
@@ -371,15 +381,24 @@
             <output name="output" file="test_bed_02_output_a__all.bed"/>
         </test>
         
-    <!-- BigWig -->
-        
+    <!-- BigWig --><!-- Malfuncioning in CrossMap 0.2
+        <test>
+            <param name="input_format" value="bigwig"/>
+            <param name="index_source" value="history"/>
+            <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/>
+            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
+            <param name="include_fails" value="False"/>
+            
+            <output name="output" file="test_bigwig_01_output_a.bw"/>
+            <output name="output2" file="test_bigwig_01_output_a.sorted.bgr"/>
+        </test>-->
     <!-- GFF -->
         <test>
             <param name="input_format" value="gff"/>
             <param name="index_source" value="history"/>
             <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
             <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
-            <param name="include_fails" value="false"/>
+            <param name="include_fails" value="False"/>
             
             <output name="output" file="test_gff_01_output_a__only-matches.gtf"/>
         </test>
@@ -388,7 +407,7 @@
             <param name="index_source" value="history"/>
             <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/>
             <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
-            <param name="include_fails" value="true"/>
+            <param name="include_fails" value="True"/>
             
             <output name="output" file="test_gff_01_output_a__all.gtf"/>
         </test>
@@ -405,10 +424,19 @@
             <output name="output" file="test_vcf_01_output.vcf" compare="diff" lines_diff="4"/>
             <output name="output_unmapped" file="test_vcf_01_output.vcf.unmap"/>
         </test>
-        
-    <!-- WIG -->
     </tests>
-    
+
+    <!-- WIG - Doesn't understand fixedStep -->
+        <test>
+            <param name="input_format" value="wig"/>
+            <param name="index_source" value="history"/>
+            <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/>
+            <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
+            <param name="include_fails" value="False"/>
+            
+            <output name="output" file="test_wig_01_output_a.bw"/>
+            <output name="output2" file="test_wig_01_output_a.sorted.bgr"/>
+        </test>
     <help>
 CrossMap is versatile tool to convert genome coordinates or annotation files between genome
 assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
diff -r 22a09104afcc -r 263581d4dd90 test-data/test_bam_01_output_a.sam
--- a/test-data/test_bam_01_output_a.sam	Thu Aug 13 07:52:11 2015 -0400
+++ b/test-data/test_bam_01_output_a.sam	Thu Aug 13 10:19:19 2015 -0400
@@ -5,7 +5,7 @@
 @SQ	SN:chr3	LN:199501827
 @SQ	SN:chr4	LN:191273063
 @PG	ID:-	VN:1.0.0	CL:cmatrix
-@PG	ID:CrossMap	VN:0.1.10
+@PG	ID:CrossMap	VN:0.2
 @CO	Test data for CrossMap bam
 @CO	Liftover from original BAM/SAM file: 
 @CO	Liftover is based on the chain file: 
diff -r 22a09104afcc -r 263581d4dd90 test-data/test_bigwig_01_input_a.bw
Binary file test-data/test_bigwig_01_input_a.bw has changed
diff -r 22a09104afcc -r 263581d4dd90 test-data/test_bigwig_01_output_a.bw
Binary file test-data/test_bigwig_01_output_a.bw has changed
diff -r 22a09104afcc -r 263581d4dd90 test-data/test_bigwig_01_output_a.sorted.bgr
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_bigwig_01_output_a.sorted.bgr	Thu Aug 13 10:19:19 2015 -0400
@@ -0,0 +1,3 @@
+chr1	889863	989862	110.0
+chr2	890000	989999	220.0
+chr3	875000	974999	330.0
diff -r 22a09104afcc -r 263581d4dd90 test-data/test_wig_01_input_a.wig
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_wig_01_input_a.wig	Thu Aug 13 10:19:19 2015 -0400
@@ -0,0 +1,10 @@
+variableStep chrom=chr1 span=900000
+100000 110
+variableStep chrom=chr2 span=900000
+100000 220
+variableStep chrom=chr3 span=900000
+100000 330
+variableStep chrom=chr4 span=50000
+9200000 400
+variableStep chrom=chr4 span=60000
+8940000 450
diff -r 22a09104afcc -r 263581d4dd90 test-data/test_wig_01_output_a.bw
Binary file test-data/test_wig_01_output_a.bw has changed
diff -r 22a09104afcc -r 263581d4dd90 test-data/test_wig_01_output_a.sorted.bgr
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_wig_01_output_a.sorted.bgr	Thu Aug 13 10:19:19 2015 -0400
@@ -0,0 +1,2 @@
+chr2	89999	989999	220.0
+chr3	74999	974999	330.0
diff -r 22a09104afcc -r 263581d4dd90 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Aug 13 07:52:11 2015 -0400
+++ b/tool_dependencies.xml	Thu Aug 13 10:19:19 2015 -0400
@@ -1,5 +1,8 @@
 <?xml version="1.0"?>
 <tool_dependency>
+    <package name="ucsc_tools" version="312"><!-- For conversion of Wig and BigWig -->
+        <repository changeset_revision="34e9010db346" name="package_ucsc_tools_312" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
     <package name="crossmap" version="0.2">
         <repository changeset_revision="1aa7754d9c75" name="package_crossmap_0_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>