diff samtools_fixmate.xml @ 0:bc0cc7bfbfe9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/samtools_fixmate.xml	Fri Sep 28 04:28:45 2018 -0400
@@ -0,0 +1,86 @@
+<tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@">
+    <description>fill mate coordinates, ISIZE and mate related flags</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @ADDTHREADS@
+        ## name sort input 
+        #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'):
+            samtools sort
+            -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
+            -n 
+            -O BAM
+            -o namesorted.bam
+            '$bamfile' &&
+        #else:
+            ln -s '$bamfile' namesorted.bam &&
+        #end if
+
+        samtools fixmate
+            -@ \$addthreads
+            $remsec
+            $noprop
+            $tempcigar
+            $addms
+            -O BAM
+            namesorted.bam
+            '$output'
+    ]]></command>
+    <inputs>
+        <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Select alignment" help="Set of aligned reads." />
+        <param name="remsec" type="boolean" argument="-r" truevalue="-r" falsevalue="" checked="false" label="Remove secondary and unmapped reads" />
+        <param name="noprop" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Disable FR proper pair check" />
+        <param name="tempcigar" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Add template cigar ct tag" />
+        <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"/>
+    </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 -");-->
+    </tests>
+    <help>
+**What it does**
+
+Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment.
+    </help>
+    <expand macro="citations"/>
+</tool>