--- a/macros_process.xml	Wed Feb 12 18:22:03 2020 -0500
+++ b/macros_process.xml	Thu Jul 16 07:32:42 2020 -0400
@@ -29,12 +29,12 @@
 
     <xml name="discover_faqgz_output_macro" token_pattern="" token_dir="">
         <expand macro="discover_faq_output_macro" pattern="@PATTERN@" dir="@DIR@"/>
-        <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/" />
-        <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/" />
+        <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/"/>
+        <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/"/>
     </xml>
     <xml name="discover_faq_output_macro" token_pattern="" token_dir="">
-        <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/" />
-        <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/" />
+        <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/"/>
+        <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/"/>
     </xml>
 
     <xml name="process_outputs">
@@ -71,17 +71,17 @@
                 <option value="no" selected="true">No</option>
             </param>
             <when value="yes">
-                <param name="sliding" type="float" value="0.15" min="0" max="1" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1" />
-                <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded" />
-                <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" />
+                <param name="sliding" type="float" value="0.15" min="0" max="1" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1"/>
+                <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded"/>
+                <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base"/>
                 <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/>
-                <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" />
+                <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"/>
             </when>
         </conditional>
-        <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
+        <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file"/>
     </xml>
     <token name="@PROCESS_FILTER@"><![CDATA[
     #if $filter_cond.filter_select == 'yes':
@@ -104,30 +104,30 @@
 
         ## fix the _R[12]_0 that was added for preparing the input
         #if $input_type.input_type_select == 'paired':
-            && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done
+            && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done)
         #end if
         ## also remove the gz which is added by procrad (but its uncompressed)
-        && find stacks_outputs/discarded/ -type f -iname "*.gz.discards" | while read file; do mv "\$file" "\$(echo \$file | sed 's/.gz.discards$/.discards/;')"; done
+        && (find stacks_outputs/discarded/ -type f -iname "*.gz.discards" | while read file; do mv "\$file" "\$(echo \$file | sed 's/.gz.discards$/.discards/;')"; done)
 
         ## the discard files are named fastq even if the output is fasta
         #if str($outype).endswith("fasta"):
-            && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fa/;')"; done
+            && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fa/;')"; done)
         #else
-            && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fq/;')"; done
+            && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fq/;')"; done)
         #end if
     #end if
     ## prepare paired read output for processing in galaxy
     #if $input_type.input_type_select == 'paired':
         && mkdir stacks_outputs/remaining
-        && find stacks_outputs -iregex ".*\.rem\.[12]\.f[aq]\(\.gz\)?" | while read file; do mv "\$file" stacks_outputs/remaining/; done
-        && find stacks_outputs/ -iregex ".*.f[aq]\(\.gz\)?" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.1\./.forward./; s/\.2\./.reverse./')"; done
+        && (find stacks_outputs -iregex ".*\.rem\.[12]\.f[aq]\(\.gz\)?" | while read file; do mv "\$file" stacks_outputs/remaining/; done)
+        && (find stacks_outputs/ -iregex ".*.f[aq]\(\.gz\)?" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.1\./.forward./; s/\.2\./.reverse./')"; done)
     #end if
     ]]></token>
 
     <!-- adapter trimming options -->
     <xml name="process_adapter">
-            <param argument="--adapter_1" type="text" value="" optional="true" label="Adaptor sequence that may occur on the first read" />
-            <param argument="--adapter_2" type="text" value="" optional="true" label="Adaptor sequence that may occur on the paired-read" />
+            <param argument="--adapter_1" type="text" value="" optional="true" label="Adaptor sequence that may occur on the first read"/>
+            <param argument="--adapter_2" type="text" value="" optional="true" label="Adaptor sequence that may occur on the paired-read"/>
             <param argument="--adapter_mm" type="integer" value="" optional="true" label="Number of mismatches allowed in the adapter sequence"/>
     </xml>
     <token name="@PROCESS_ADAPTER@"><![CDATA[
@@ -171,8 +171,8 @@
 
     <!-- advanced options that are shared -->
     <xml name="common_advanced">
-        <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" />
-        <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output" />
+        <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value"/>
+        <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output"/>
     </xml>
     <token name="@COMMON_ADVANCED@"><![CDATA[
     #if str($options_advanced.truncate)
@@ -181,3 +181,4 @@
     $options_advanced.retain_header
     ]]></token>
 </macros>
+