diff macros_process.xml @ 5:887e0991eb24 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 16654f3b3faaba994cea5fda8d4907ea4f059605"

--- a/macros_process.xml	Wed Sep 01 11:31:54 2021 +0000
+++ b/macros_process.xml	Thu Apr 14 09:23:35 2022 +0000
@@ -4,14 +4,17 @@
 
 <macros>
 
+  
     <token name="@PROCESS_IOOPTIONS@"><![CDATA[
     -p stacks_inputs/
     #if $input_type.input_type_select == "paired"
         --paired
     #end if
     -i $inputype
-    -b '$barcode'
     $input_type.barcode_encoding
+    #if $input_type.barcode_encoding != ''
+        -b '$input_type.barcode'
+    #end if
     #if str( $outype ) != "auto"
         -y $outype
     #end if
@@ -38,20 +41,11 @@
     </xml>
 
     <xml name="process_outputs">
-        <collection name="demultiplexed" type="list" label="${tool.name} on ${on_string} Demultiplexed reads">
-            <filter>input_type['input_type_select'] == "single"</filter>
-            <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;name&gt;.+)" dir="stacks_outputs"/>
-        </collection>
-        <collection name="demultiplexed_paired" type="list:paired" label="${tool.name} on ${on_string} Demultiplexed reads">
-            <filter>input_type['input_type_select'] == "paired"</filter>
-            <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs"/>
-        </collection>
-
+        <yield/>
         <collection name="remaining" type="list:paired" label="${tool.name} on ${on_string} Remaining orphan reads">
             <filter>input_type['input_type_select'] == "paired"</filter>
             <expand macro="discover_faqgz_output_macro" pattern="(?P&lt;identifier_0&gt;.+)\.rem\.(?P&lt;identifier_1&gt;[^.]+)" dir="stacks_outputs/remaining"/>
         </collection>
-
         <!-- note irrespective of -y output is always named fastq and are never zipped -->
         <collection name="discarded" type="list" label="${tool.name} on ${on_string} Discarded reads">
             <filter>capture is True and input_type['input_type_select'] == "single"</filter>
@@ -78,7 +72,7 @@
                 <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing"/>
             </when>
             <when value="no">
-                <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="useful if your data has already been trimmed"/>
+                <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="Useful if your data has already been trimmed"/>
             </when>
         </conditional>
         <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file"/>