comparison samtools_markdup.xml @ 0:046cbf29795a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_markdup commit 0fe00966500158720fb63dc9b28f6a4ca0d1e1eb
author iuc
date Fri, 28 Sep 2018 04:29:07 -0400
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children 83b8e36e9cbe
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-1:000000000000 0:046cbf29795a
1 <tool id="samtools_markdup" name="Samtools markdup" version="@TOOL_VERSION@">
2 <description>marks duplicate alignments</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
8 <expand macro="version_command"/>
9 <command><![CDATA[
10 @ADDTHREADS@
11 ## coordinate sort input
12 #if not $bamfile.is_of_type('bam'):
13 samtools sort
14 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
15 -O sam
16 -o coordsort.sam
17 '$bamfile' &&
18 #else:
19 ln -s '$bamfile' coordsort.sam &&
20 #end if
21
22 samtools markdup
23
24 -@ \$addthreads
25 #if str($maxlen) != '':
26 -l $maxlen
27 #end if
28 $remove
29 $stats
30 $supp
31 coordsort.sam
32 '$output'
33 ]]></command>
34 <inputs>
35 <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Alignment" />
36 <param name="remove" type="boolean" argument="-r" truevalue="-r" falsevalue="" label="Remove duplicate reads" />
37 <param name="maxlen" type="integer" optional="true" argument="-l" min="0" label="Expected maximum read length of INT bases. (default 300)"/>
38 <param name="stats" type="boolean" argument="-s" truevalue="-s" falsevalue="" label="Print basic statistics" />
39 <param name="supp" type="boolean" argument="-S" truevalue="-S" falsevalue="" label="Mark supplementary reads of duplicates as duplicates" />
40 </inputs>
41 <outputs>
42 <!-- output bam, if input was name sorted then restore this sorting order -->
43 <data name="output" format="bam"/>
44 </outputs>
45 <tests>
46 <!-- tests and data extracted from
47 https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2616
48 TODO the 1st 4 tests are negative, I do not know how to test for the error code
49 -->
50 <!-- 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);
51 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);
52 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);
53 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);-->
54 <test>
55 <param name="bamfile" value="5_markdup.sam" />
56 <output name="output" file="5_markdup.expected.bam" />
57 </test>
58 <!-- test_cmd($opts, out=>'markdup/5_markdup.expected.sam', cmd=>"$$opts{bin}/samtools markdup${threads} -O sam $$opts{path}/markdup/5_markdup.sam -");-->
59 <test>
60 <param name="bamfile" value="6_remove_dups.sam" />
61 <param name="remove" value="-r" />
62 <output name="output" file="6_remove_dups.expected.bam" />
63 </test>
64 <!-- 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 -");-->
65 <test>
66 <param name="bamfile" value="7_mark_supp_dup.bam" />
67 <param name="supp" value="-S" />
68 <output name="output" file="7_mark_supp_dup.expected.bam" />
69 </test>
70 <!--
71 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 -");-->
72 </tests>
73 <help>
74 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.
75
76 Note: The Galaxy tool sorts the data automatically if the input is SAM or query name sorted.
77 The output is BAM (which is query name sorted again if the input is).
78 </help>
79 <expand macro="citations"/>
80 </tool>