diff chira_collapse.xml @ 15:00187b27f5e5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 030e4e8e72dc37ccd64702e093e949d18899ad73"

--- a/chira_collapse.xml	Sat Aug 15 19:07:21 2020 -0400
+++ b/chira_collapse.xml	Wed Apr 07 12:41:46 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="chira_collapse" name="ChiRA collapse" version="@WRAPPER_VERSION@0">
+<tool id="chira_collapse" name="ChiRA collapse" version="@WRAPPER_VERSION@1">
     <description>deduplicate fastq reads</description>
     <macros>
         <import>macros.xml</import>
@@ -6,13 +6,18 @@
     <expand macro="requirements" />    
     <command><![CDATA[
         chira_collapse.py
-        -i '$in'
+        -i 
+        #if $in.ext.endswith(".gz")
+            <(gunzip -c '$in')
+        #else
+            '$in'
+        #end if
         -u '$umi_len'
         -o '$out'
     ]]></command>
 
     <inputs>
-        <param format="fastq" name="in" type="data" label="Input FASTQ file"/>
+        <param format="fastq,fastq.gz" name="in" type="data" label="Input FASTQ file"/>
         <param name="umi_len" type="integer" value="0"
                label="Length of the UMI if present at the 5' end of your reads"/>
     </inputs>
@@ -22,7 +27,7 @@
 
     <tests>
         <test expect_num_outputs="1">
-            <param name="in" value="reads.fastq" />
+            <param name="in" value="reads.fastq.gz" ftype="fastq.gz"/>
             <output name="out" file="reads.fasta" />
         </test>
     </tests>