changeset 5:da00153634dc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_barcode_splitter commit b2735803f9719ff955a49a5bde54a211d6d48bb5

--- a/fastx_barcode_splitter.xml	Tue May 08 12:50:59 2018 -0400
+++ b/fastx_barcode_splitter.xml	Thu Oct 11 09:35:34 2018 -0400
@@ -8,7 +8,18 @@
 mkdir split &&
 @CATS@ '$__tool_directory__/fastx_barcode_splitter.pl' --bcfile '$BARCODE'
 --prefix 'split/'
---suffix '.$input.extension'
+--suffix 
+#if $input.is_of_type('fastqsanger', 'fastqsanger.gz', 'fastqsanger.bz2'):
+    '.fastqsanger'
+#elif $input.is_of_type('fastqsolexa', 'fastqsolexa.gz', 'fastqsolexa.bz2'):
+    '.fastqsolexa'
+#elif $input.is_of_type('fastqillumina', 'fastqillumina.gz', 'fastqillumina.bz2'):
+    '.fastqillumina'
+#elif $input.is_of_type('fasta', 'fasta.gz'):
+    '.fasta'
+#else:
+    '.$input.extension'
+#end if
 --mismatches $mismatches
 --partial $partial
 #if $refBarcodeLocation.barcodeLocation == "idxfile":
@@ -21,8 +32,7 @@
     ]]></command>
     <inputs>
         <param name="BARCODE" type="data" format="txt" label="Barcodes to use" />
-        <param name="input" type="data" format="fasta,fastq,fastqsanger,fastqsolexa,fastqillumina" label="Library to split" />
-
+        <param name="input" type="data" format="@FASTAS@,@FASTQS@,fastq" label="Library to split" />
         <conditional name="refBarcodeLocation">
             <param name="barcodeLocation" type="select" label="Barcodes found at">
                 <option value="bol">Start of sequence (5' end)</option>
@@ -46,7 +56,7 @@
 
     <outputs>
         <data name="summary" format="tabular" label="${tool.name} on ${on_string}: Summary" />
-        <collection name="split_output" type="list" format_source="input" label="${tool.name} on ${on_string}">
+        <collection name="split_output" type="list" label="${tool.name} on ${on_string}">
             <discover_datasets pattern="__designation_and_ext__" directory="split" visible="false" />
         </collection>
     </outputs>
@@ -68,6 +78,23 @@
                 <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
             </output_collection>
         </test>
+        
+        <test>
+          <!-- Split a FASTQ.gz file -->
+          <param name="BARCODE" value="fastx_barcode_splitter1.txt" />
+          <param name="input" value="fastx_barcode_splitter1.fastq.gz" ftype="fastqsolexa.gz" />
+          <param name="barcodeLocation" value="bol" />
+          <param name="mismatches" value="2" />
+          <param name="partial" value="0" />
+          <output name="summary" file="fastx_barcode_splitter1.out" />
+          <output_collection name="split_output" type="list">
+            <element name="BC1" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC1.out" />
+            <element name="BC2" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC2.out" />
+            <element name="BC3" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC3.out" />
+            <element name="BC4" ftype="fastqsolexa" file="fastx_barcode_splitter1_BC4.out" />
+            <element name="unmatched" ftype="fastqsolexa" file="fastx_barcode_splitter1_unmatched.out" />
+          </output_collection>
+        </test>
 
         <test>
             <!-- Split a FASTQ file, using separate index read -->

--- a/macros.xml	Tue May 08 12:50:59 2018 -0400
+++ b/macros.xml	Thu Oct 11 09:35:34 2018 -0400
@@ -2,7 +2,7 @@
 <macros>
     <token name="@CATS@">
         #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
-            zcat -f '$input' |
+            gunzip -c -f '$input' |
         #elif $input.is_of_type('fastqsanger.bz2', 'fastqsolexa.bz2', 'fastqillumina.bz2'):
             bzcat -f '$input' |
         #else:
@@ -18,6 +18,13 @@
             #end if
         ]]>
     </token>
+    <token name="@GZIP@">
+        <![CDATA[
+            #if $input.is_of_type('fasta.gz', 'fastqsanger.gz', 'fastqsolexa.gz', 'fastqillumina.gz'):
+                -z
+            #end if
+        ]]>
+    </token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@VERSION@">fastx_toolkit</requirement>

Binary file test-data/fastx_barcode_splitter1.fastq.gz has changed