diff hisat2_macros.xml @ 10:da8d655e2154 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit d3803bf87eb04a8c2a239e270c8c5c0596277890

--- a/hisat2_macros.xml	Tue Apr 04 08:15:43 2017 -0400
+++ b/hisat2_macros.xml	Mon Apr 10 17:40:42 2017 -0400
@@ -33,8 +33,8 @@
             </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" />
+                <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 / --un-gz" />
+                <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 / --al-gz" />
             </when>
         </conditional>
     </xml>
@@ -55,15 +55,23 @@
         </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" />
+        <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 / --un-conc-gz" />
+        <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 / --al-conc-gz" />
     </xml>
     <token name="@paired_end_options@">
         #if str( $input_format.paired.unaligned_file ) == "true":
-            --un-conc '${output_unaligned_reads_l}'
+            #if $compressed == "GZ":
+                --un-conc-gz '${output_unaligned_reads_l}'
+            #else:
+                --un-conc '${output_unaligned_reads_l}'
+            #end if
         #end if
         #if str( $input_format.paired.aligned_file ) == "true":
-            --al-conc '${output_aligned_reads_l}'
+            #if $compressed == "GZ":
+                --al-conc '${output_aligned_reads_l}'
+            #else:
+                --al-conc '${output_aligned_reads_l}'
+            #end if
         #end if  
         #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced':
             ${input_format.paired.paired_end_options.no_mixed}
@@ -77,4 +85,65 @@
             #end if
         #end if
     </token>
+    <token name="@FASTQGZ_SETUP@">
+<![CDATA[
+        #set compressed="False"
+        #if str($input_format.paired.paired_selector) == 'paired':
+            #if $input_format.paired.reads_f.is_of_type("fastq.gz", "fastqsanger.gz"):
+                #set read1 = "input_f.fastq.gz"
+                #set compressed = "GZ"
+            #else if $input_format.paired.reads_f.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+                #set read1 = "input_f.fastq.bz2"
+                #set compressed = "BZ2"
+            #else:
+                #set read1 = "input_f.fastq"
+            #end if
+            ln -f -s "${input_format.paired.reads_f}" "${read1}" &&
+
+            #if $input_format.paired.reads_r.is_of_type("fastq.gz", "fastqsanger.gz"):
+                #set read2 = "input_r.fastq.gz"
+                #set compressed = "GZ"
+            #else if $input_format.paired.reads_r.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+                #set read2 = "input_r.fastq.bz2"
+                #set compressed = "BZ2"
+            #else:
+                #set read2 = "input_r.fastq"
+            #end if
+            ln -f -s "${input_format.paired.reads_r}" "${read2}" &&
+        #else if str($input_format.paired.paired_selector) == 'paired_collection':
+            #if $input_format.paired.reads.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
+                #set read1 = "input_f.fastq.gz"
+                #set compressed = "GZ"
+            #else if $input_format.paired.reads.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+                #set read1 = "input_f.fastq.bz2"
+                #set compressed = "BZ2"
+            #else:
+                #set read1 = "input_f.fastq"
+            #end if
+            ln -s "${input_format.paired.reads.forward}" "${read1}" &&
+
+            #if $input_format.paired.reads.reverse.is_of_type("fastq.gz", "fastqsanger.gz"):
+                #set read2 = "input_r.fastq.gz"
+                #set compressed = "GZ"
+            #else if $input_format.paired.reads.reverse.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+                #set read2 = "input_r.fastq.bz2"
+                #set compressed = "BZ2"
+            #else:
+                #set read2 = "input_r.fastq"
+            #end if
+            ln -s "${input_format.paired.reads.reverse}" "${read2}" &&
+        #else:
+            #if $input_format.paired.reads.is_of_type("fastq.gz", "fastqsanger.gz"):
+                #set read1 = "input_f.fastq.gz"
+                #set compressed = "GZ"
+            #else if $input_format.paired.reads.is_of_type("fastq.bz2", "fastqsanger.bz2"):
+                #set read1 = "input_f.fastq.bz2"
+                #set compressed = "BZ2"
+            #else:
+                #set read1 = "input_f.fastq"
+            #end if
+            ln -s "${input_format.paired.reads}" "${read1}" &&
+        #end if
+]]>
+    </token>
 </macros>