diff hisat2_macros.xml @ 7:5ba8e317529a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit 5c49c4049418cdca86f40df5a5d8014c2d932dde

--- a/hisat2_macros.xml	Wed Nov 09 05:57:35 2016 -0500
+++ b/hisat2_macros.xml	Sat Jan 21 15:42:34 2017 -0500
@@ -23,14 +23,18 @@
             <when value="paired_collection">
                 <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" />
                 <expand macro="paired_end_conditional" />
+                <expand macro="paired_end_output" />
             </when>
             <when value="paired">
                 <param format="@FTYPE@" label="Forward reads" name="reads_f" type="data" />
                 <param format="@FTYPE@" label="Reverse reads" name="reads_r" type="data" />
                 <expand macro="paired_end_conditional" />
+                <expand macro="paired_end_output" />
             </when>
             <when value="single">
                 <param format="@FTYPE@" label="Reads" name="reads" type="data" />
+                <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un" />
+                <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al" />
             </when>
         </conditional>
     </xml>
@@ -50,7 +54,17 @@
             </when>
         </conditional>
     </xml>
+    <xml name="paired_end_output">
+        <param name="unaligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write unaligned reads (in fastq format) to separate file(s)" argument="--un-conc" />
+        <param name="aligned_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write aligned reads (in fastq format) to separate file(s)" argument="--al-conc" />
+    </xml>
     <token name="@paired_end_options@">
+        #if str( $input_format.paired.unaligned_file ) == "true":
+            --un-conc '${output_unaligned_reads_l}'
+        #end if
+        #if str( $input_format.paired.aligned_file ) == "true":
+            --al-conc '${output_aligned_reads_l}'
+        #end if  
         #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced':
             ${input_format.paired.paired_end_options.no_mixed}
             ${input_format.paired.paired_end_options.no_discordant}