diff seqtk_mergepe.xml @ 16:48a51c72f5e7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2

--- a/seqtk_mergepe.xml	Mon Jun 05 13:26:30 2017 -0400
+++ b/seqtk_mergepe.xml	Wed Oct 17 05:58:58 2018 -0400
@@ -10,20 +10,25 @@
 seqtk mergepe
 '$in_fq1'
 '$in_fq2'
-> '$default'
+ #echo "| gzip --no-name" if $in_fq1.is_of_type('fasta.gz', 'fastq.gz') else "" # > '$default'
     ]]></command>
     <inputs>
-        <param name="in_fq1" type="data" format="fasta,fastq" label="Input FASTA/Q file #1"/>
-        <param name="in_fq2" type="data" format="fasta,fastq" label="Input FASTA/Q file #2"/>
+        <param name="in_fq1" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #1"/>
+        <param name="in_fq2" type="data" format="fasta,fastq,fasta.gz,fastq.gz" label="Input FASTA/Q file #2"/>
     </inputs>
     <outputs>
         <data name="default" format_source="in_fq1" label="$in_fq1.name and $in_fq2.name as interleaved paired-end"/>
     </outputs>
     <tests>
         <test>
-            <param name="in_fq1" value="paired_dat1.fq"/>
-            <param name="in_fq2" value="paired_dat2.fq"/>
-            <output name="default" file="paired_dat.fq" ftype="fastq"/>
+            <param name="in_fq1" value="paired_dat1.fq" ftype="fastqsanger"/>
+            <param name="in_fq2" value="paired_dat2.fq" ftype="fastqsanger"/>
+            <output name="default" file="paired_dat.fq" ftype="fastqsanger"/>
+        </test>
+        <test>
+            <param name="in_fq1" value="paired_dat1.fq.gz" ftype="fastqsanger.gz"/>
+            <param name="in_fq2" value="paired_dat2.fq.gz" ftype="fastqsanger.gz"/>
+            <output name="default" file="paired_dat.fq.gz" ftype="fastqsanger.gz"/>
         </test>
     </tests>
     <help><![CDATA[