Mercurial > repos > iuc > samtools_markdup
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 |
parents | |
children | 83b8e36e9cbe |
comparison
equal
deleted
inserted
replaced
-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> |