diff samtools_fixmate.xml @ 1:595ae1ba934a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"

--- a/samtools_fixmate.xml	Fri Sep 28 04:28:45 2018 -0400
+++ b/samtools_fixmate.xml	Tue Sep 28 16:13:23 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@">
+<tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@" profile="@PROFILE@">
     <description>fill mate coordinates, ISIZE and mate related flags</description>
     <macros>
         <import>macros.xml</import>
@@ -8,11 +8,11 @@
     <expand macro="version_command"/>
     <command><![CDATA[
         @ADDTHREADS@
-        ## name sort input 
+        ## name sort input
         #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'):
             samtools sort
-            -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
-            -n 
+            -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
+            -n
             -O BAM
             -o namesorted.bam
             '$bamfile' &&
@@ -38,44 +38,44 @@
         <param name="addms" type="boolean" argument="-m" truevalue="-m" falsevalue="" checked="false" label="Add ms (mate score) tags" help="These are used by markdup to select the best reads to keep." />
     </inputs>
     <outputs>
-	<!--<data name="output" format="sam" />-->
-	<data name="output" format="qname_sorted.bam"/>
+	   <!--<data name="output" format="sam" />-->
+	   <data name="output" format="qname_sorted.bam"/>
     </outputs>
     <tests>
-<!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493-->
-<!--    test_cmd($opts,out=>'fixmate/1_coord_sort.sam.expected', err=>'fixmate/1_coord_sort.sam.expected.err', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/1_coord_sort.sam -", expect_fail=>1);-->
-<test>
-    <param name="bamfile" value="2_isize_overflow.sam" />
-    <output name="output" file="2_isize_overflow.bam.expected" />
-</test>
-<!--    test_cmd($opts,out=>'fixmate/2_isize_overflow.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/2_isize_overflow.sam -");-->
-<test>
-    <param name="bamfile" value="3_reverse_read_pp_lt.sam" />
-    <output name="output" file="3_reverse_read_pp_lt.bam.expected" />
-</test>
-<!--    test_cmd($opts,out=>'fixmate/3_reverse_read_pp_lt.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/3_reverse_read_pp_lt.sam -");-->
-<test>
-    <param name="bamfile" value="4_reverse_read_pp_equal.sam" />
-    <output name="output" file="4_reverse_read_pp_equal.bam.expected" />
-</test>
-<!--    test_cmd($opts,out=>'fixmate/4_reverse_read_pp_equal.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/4_reverse_read_pp_equal.sam -");-->
-<test>
-    <param name="bamfile" value="5_ct.sam" />
-    <param name="tempcigar" value="-c" />
-    <output name="output" file="5_ct.bam.expected" />
-</test>
-<!--    test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");-->
-<test>
-    <param name="bamfile" value="6_ct_replace.sam" />
-    <param name="tempcigar" value="-c" />
-    <output name="output" file="6_ct_replace.bam.expected" />
-</test>
-<!--    test_cmd($opts,out=>'fixmate/6_ct_replace.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/6_ct_replace.sam -");-->
-<test>
-    <param name="bamfile" value="7_two_read_mapped.sam" />
-    <output name="output" file="7_two_read_mapped.bam.expected" />
-</test>
-<!--test_cmd($opts,out=>'fixmate/7_two_read_mapped.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/7_two_read_mapped.sam -");-->
+        <!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493-->
+        <!--    test_cmd($opts,out=>'fixmate/1_coord_sort.sam.expected', err=>'fixmate/1_coord_sort.sam.expected.err', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/1_coord_sort.sam -", expect_fail=>1);-->
+        <test>
+            <param name="bamfile" value="2_isize_overflow.sam" ftype="sam" />
+            <output name="output" file="2_isize_overflow.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
+        </test>
+        <!--    test_cmd($opts,out=>'fixmate/2_isize_overflow.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/2_isize_overflow.sam -");-->
+        <test>
+            <param name="bamfile" value="3_reverse_read_pp_lt.sam" ftype="sam" />
+            <output name="output" file="3_reverse_read_pp_lt.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
+        </test>
+        <!--    test_cmd($opts,out=>'fixmate/3_reverse_read_pp_lt.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/3_reverse_read_pp_lt.sam -");-->
+        <test>
+            <param name="bamfile" value="4_reverse_read_pp_equal.sam" ftype="sam" />
+            <output name="output" file="4_reverse_read_pp_equal.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
+        </test>
+        <!--    test_cmd($opts,out=>'fixmate/4_reverse_read_pp_equal.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/4_reverse_read_pp_equal.sam -");-->
+        <test>
+            <param name="bamfile" value="5_ct.sam" ftype="sam" />
+            <param name="tempcigar" value="-c" />
+            <output name="output" file="5_ct.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
+        </test>
+        <!--    test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");-->
+        <test>
+            <param name="bamfile" value="6_ct_replace.sam" ftype="sam" />
+            <param name="tempcigar" value="-c" />
+            <output name="output" file="6_ct_replace.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
+        </test>
+        <!--    test_cmd($opts,out=>'fixmate/6_ct_replace.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/6_ct_replace.sam -");-->
+        <test>
+            <param name="bamfile" value="7_two_read_mapped.sam" ftype="sam" />
+            <output name="output" file="7_two_read_mapped.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
+        </test>
+        <!--test_cmd($opts,out=>'fixmate/7_two_read_mapped.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -O sam $$opts{path}/fixmate/7_two_read_mapped.sam -");-->
     </tests>
     <help>
 **What it does**