# HG changeset patch
# User iuc
# Date 1567766126 14400
# Node ID 83b8e36e9cbe7a6316f9fc95df8b6615be33c251
# Parent  046cbf29795a984871a227a7cc5c35176edbd3f1
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 91b28adf44f425970469cc52fc5c13e75409ed27"

diff -r 046cbf29795a -r 83b8e36e9cbe samtools_markdup.xml
--- a/samtools_markdup.xml	Fri Sep 28 04:29:07 2018 -0400
+++ b/samtools_markdup.xml	Fri Sep 06 06:35:26 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@">
+<tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@+galaxy2">
     <description>marks duplicate alignments</description>
     <macros>
         <import>macros.xml</import>
@@ -11,7 +11,7 @@
 ## coordinate sort input 
 #if not $bamfile.is_of_type('bam'):
     samtools sort
-    -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
+    -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
     -O sam
     -o coordsort.sam
     '$bamfile' &&
@@ -30,51 +30,66 @@
 $supp
 coordsort.sam 
 '$output'
+#if $stats
+    2> '$stats_output'
+#end if
     ]]></command>
     <inputs>
         <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Alignment" />
         <param name="remove" type="boolean" argument="-r" truevalue="-r" falsevalue="" label="Remove duplicate reads" />
         <param name="maxlen" type="integer" optional="true" argument="-l" min="0" label="Expected maximum read length of INT bases. (default 300)"/>
-	<param name="stats" type="boolean" argument="-s" truevalue="-s" falsevalue="" label="Print basic statistics" />
-	<param name="supp" type="boolean" argument="-S" truevalue="-S" falsevalue="" label="Mark supplementary reads of duplicates as duplicates" />
+        <param name="stats" type="boolean" argument="-s" truevalue="-s" falsevalue="" label="Print basic statistics" />
+        <param name="supp" type="boolean" argument="-S" truevalue="-S" falsevalue="" label="Mark supplementary reads of duplicates as duplicates" />
     </inputs>
     <outputs>
-	<!-- output bam, if input was name sorted then restore this sorting order -->
-	<data name="output" format="bam"/>
+        <!-- output bam, if input was name sorted then restore this sorting order -->
+        <data name="output" format="bam"/>
+        <data name="stats_output" format="txt">
+            <filter>stats</filter>
+        </data>
     </outputs>
     <tests>
         <!-- tests and data extracted from 
-	     https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2616 
+             https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2616 
              TODO the 1st 4 tests are negative, I do not know how to test for the error code 
 -->
 <!--    test_cmd($opts, out=>'markdup/1_name_sort.expected.sam', err=>'1_name_sort.expected.sam.err', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/1_name_sort.sam -", expect_fail=>1);
     test_cmd($opts, out=>'markdup/2_bad_order.expected.sam', err=>'2_bad_order.expected.sam.err', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/2_bad_order.sam -", expect_fail=>1);
     test_cmd($opts, out=>'markdup/3_missing_mc.expected.sam', err=>'3_missing_mc.expected.sam.err', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/3_missing_mc.sam -", expect_fail=>1);
     test_cmd($opts, out=>'markdup/4_missing_ms.expected.sam', err=>'4_missing_ms.expected.sam.err', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/4_missing_ms.sam -", expect_fail=>1);-->
-        <test>
+        <!--    test_cmd($opts, out=>'markdup/5_markdup.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/5_markdup.sam -");-->
+        <test expect_num_outputs="1">
             <param name="bamfile" value="5_markdup.sam" />
             <output name="output" file="5_markdup.expected.bam" />
         </test>
-        <!--    test_cmd($opts, out=>'markdup/5_markdup.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/5_markdup.sam -");-->
-        <test>
+        <!--    test_cmd($opts, out=>'markdup/6_remove_dups.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam -r $$opts{path}/markdup/6_remove_dups.sam -");-->
+        <test expect_num_outputs="1">
             <param name="bamfile" value="6_remove_dups.sam" />
             <param name="remove" value="-r" />
             <output name="output" file="6_remove_dups.expected.bam" />
         </test>
-        <!--    test_cmd($opts, out=>'markdup/6_remove_dups.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam -r $$opts{path}/markdup/6_remove_dups.sam -");-->
-        <test>
+        <!-- test_cmd($opts, out=>'markdup/7_mark_supp_dup.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -S -O sam $$opts{path}/markdup/7_mark_supp_dup.sam -");-->
+        <test expect_num_outputs="1">
             <param name="bamfile" value="7_mark_supp_dup.bam" />
             <param name="supp" value="-S" />
             <output name="output" file="7_mark_supp_dup.expected.bam" />
         </test>
-        <!--
-        test_cmd($opts, out=>'markdup/7_mark_supp_dup.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -S -O sam $$opts{path}/markdup/7_mark_supp_dup.sam -");-->
+        <!-- test stats output -->
+        <test expect_num_outputs="2">
+            <param name="bamfile" value="5_markdup.sam" />
+            <param name="stats" value="-s" />
+            <output name="output" file="5_markdup.expected.bam" />
+            <output name="stats_output" file="stats.txt" />
+        </test>
     </tests>
     <help>
 Mark duplicate alignments from a coordinate sorted file that has been run through fixmate with the -m option. This program relies on the MC and ms tags that fixmate provides. 
 
 Note: The Galaxy tool sorts the data automatically if the input is SAM or query name sorted. 
 The output is BAM (which is query name sorted again if the input is).
-    </help>
+
+The optional basic statistics output of samtools markdup can be visualized with MultiQC.
+
+	</help>
     <expand macro="citations"/>
 </tool>
diff -r 046cbf29795a -r 83b8e36e9cbe test-data/stats.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/stats.txt	Fri Sep 06 06:35:26 2019 -0400
@@ -0,0 +1,5 @@
+READ 16 WRITTEN 16 
+EXCLUDED 3 EXAMINED 13
+PAIRED 10 SINGLE 3
+DULPICATE PAIR 4 DUPLICATE SINGLE 2
+DUPLICATE TOTAL 6