# HG changeset patch
# User dfornika
# Date 1583882408 0
# Node ID 97b21fddeff79af3f794f740ed48786f5d0f14b5
# Parent  26516cf264447479096a0fffb904dc7cc284a959
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"

diff -r 26516cf26444 -r 97b21fddeff7 artic_align_trim.xml
--- a/artic_align_trim.xml	Tue Mar 10 22:52:48 2020 +0000
+++ b/artic_align_trim.xml	Tue Mar 10 23:20:08 2020 +0000
@@ -6,13 +6,20 @@
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         python '${__tool_directory__}/align_trim.py'
-             '${primer_scheme_bedfile.fields.path}'
-             --start 
-             --report '${start_trim_report}'
-             < '${input_alignment}'
-             2> '${start_trim_err}' |
+            '${primer_scheme_bedfile.fields.path}'
+            --start 
+            --report '${start_trim_report}'
+            < '${input_alignment}'
+            2> '${start_trim_err}' |
         samtools view -bS - |
-        samtools sort - -o '${trimmed_sorted_alignment}' 
+        samtools sort - -o '${start_trimmed_sorted_alignment}' &&
+        python '${__tool_directory__}/align_trim.py'
+            '${primer_scheme_bedfile.fields.path}'
+            --report '${end_trim_report}'
+            < '${input_alignment}'
+            2> '${end_trim_err}' |
+        samtools view -bS - |
+        samtools sort - -o '${end_trimmed_sorted_alignment}' &&
     ]]></command>
     <inputs>
         <param name="input_alignment" type="data" format="bam" label="Input Alignment"/>
@@ -23,9 +30,12 @@
 	</param>
     </inputs>
     <outputs>
-        <data name="start_trim_report" format="txt" label="Alignment Report" />
-        <data name="start_trim_err" format="txt" label="Alignment Error Report" />
-        <data name="trimmed_sorted_alignment" format="bam" />
+        <data name="start_trim_report" format="txt" label="Report (Trim to start of primers)" />
+        <data name="start_trim_err" format="txt" label="Error Report (Trim to start of primers)" />
+        <data name="end_trim_report" format="txt" label="Report (Trim to end of primers)" />
+        <data name="end_trim_err" format="txt" label="Error Report (Trim to end of primers)" />
+        <data name="start_trimmed_sorted_alignment" format="bam" label="Trimmed Alignment (Trim to start of primers)" />
+        <data name="end_trimmed_sorted_alignment" format="bam" label="Trimmed Alignment (Trim to end of primers)" />
     </outputs>
     <tests>
     </tests>