diff bamToFastq.xml @ 34:dde39ba9c031 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95

--- a/bamToFastq.xml	Mon Dec 17 14:23:31 2018 -0500
+++ b/bamToFastq.xml	Mon Apr 29 05:55:48 2019 -0400
@@ -1,28 +1,28 @@
-<tool id="bedtools_bamtofastq" name="bedtools Convert from BAM to FastQ" version="@WRAPPER_VERSION@">
+<tool id="bedtools_bamtofastq" name="bedtools Convert from BAM to FastQ" version="@TOOL_VERSION@">
     <description></description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <expand macro="stdio" />
-    <command>
-        bedtools bamtofastq
-        $tags
-        -i '$input'
-        -fq '$output'
-        #if $fq2:
-           -fq2 '$output2'
-        #end if
-    </command>
+    <command><![CDATA[
+bedtools bamtofastq
+$tags
+-i '$input'
+-fq '$output'
+#if $fq2:
+    -fq2 '$output2'
+#end if
+    ]]></command>
     <inputs>
-        <param format="bam" name="input" type="data" label="Convert the following BAM file to FASTQ"/>
-        <param name="tags" type="boolean" truevalue="-tags" falsevalue="" checked="False" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
-        <param name="fq2" type="boolean" truevalue="-fq2" falsevalue="" checked="False" label="FASTQ for second end.
-            Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
+        <param name="input" type="data" format="bam" label="Convert the following BAM file to FASTQ"/>
+        <param argument="-tags" type="boolean" truevalue="-tags" falsevalue="" checked="false" label="Create FASTQ based on the mate info in the BAM R2 and Q2 tags."/>
+        <param argument="-fq2" type="boolean" truevalue="-fq2" falsevalue="" checked="false" label="FASTQ for second end"
+            help="Used if BAM contains paired-end data. BAM should be sorted by query name if creating paired FASTQ with this option."/>
     </inputs>
     <outputs>
-        <data format="fastq" name="output" metadata_source="input" label="${input.name} (as FASTQ)"/>
-        <data format="fastq" name="output2" metadata_source="input" label="${input.name} (as FASTQ)">
+        <data name="output" format="fastq" metadata_source="input" label="${input.name} (as FASTQ)"/>
+        <data name="output2" format="fastq" metadata_source="input" label="${input.name} (as FASTQ)">
             <filter>fq2 is True</filter>
         </data>
     </outputs>
@@ -32,14 +32,12 @@
             <output name="output" file="bamToFastq_result1.fastq" ftype="fastq" />
         </test>
     </tests>
-<help>
-
+    <help><![CDATA[
 **What it does**
 
 bedtools bamtofastq is a conversion utility for extracting FASTQ records from sequence alignments in BAM format.
 
 @REFERENCES@
-
-    </help>
+    ]]></help>
     <expand macro="citations" />
 </tool>