Mercurial > repos > iuc > samtools_fixmate
comparison 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
author | iuc |
---|---|
date | Fri, 28 Sep 2018 04:28:45 -0400 |
parents | |
children | 595ae1ba934a |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:bc0cc7bfbfe9 |
---|---|
1 <tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@"> | |
2 <description>fill mate coordinates, ISIZE and mate related flags</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 ## name sort input | |
12 #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'): | |
13 samtools sort | |
14 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp | |
15 -n | |
16 -O BAM | |
17 -o namesorted.bam | |
18 '$bamfile' && | |
19 #else: | |
20 ln -s '$bamfile' namesorted.bam && | |
21 #end if | |
22 | |
23 samtools fixmate | |
24 -@ \$addthreads | |
25 $remsec | |
26 $noprop | |
27 $tempcigar | |
28 $addms | |
29 -O BAM | |
30 namesorted.bam | |
31 '$output' | |
32 ]]></command> | |
33 <inputs> | |
34 <param name="bamfile" type="data" format="sam,bam,cram" optional="false" label="Select alignment" help="Set of aligned reads." /> | |
35 <param name="remsec" type="boolean" argument="-r" truevalue="-r" falsevalue="" checked="false" label="Remove secondary and unmapped reads" /> | |
36 <param name="noprop" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Disable FR proper pair check" /> | |
37 <param name="tempcigar" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Add template cigar ct tag" /> | |
38 <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." /> | |
39 </inputs> | |
40 <outputs> | |
41 <!--<data name="output" format="sam" />--> | |
42 <data name="output" format="qname_sorted.bam"/> | |
43 </outputs> | |
44 <tests> | |
45 <!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493--> | |
46 <!-- 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);--> | |
47 <test> | |
48 <param name="bamfile" value="2_isize_overflow.sam" /> | |
49 <output name="output" file="2_isize_overflow.bam.expected" /> | |
50 </test> | |
51 <!-- 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 -");--> | |
52 <test> | |
53 <param name="bamfile" value="3_reverse_read_pp_lt.sam" /> | |
54 <output name="output" file="3_reverse_read_pp_lt.bam.expected" /> | |
55 </test> | |
56 <!-- 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 -");--> | |
57 <test> | |
58 <param name="bamfile" value="4_reverse_read_pp_equal.sam" /> | |
59 <output name="output" file="4_reverse_read_pp_equal.bam.expected" /> | |
60 </test> | |
61 <!-- 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 -");--> | |
62 <test> | |
63 <param name="bamfile" value="5_ct.sam" /> | |
64 <param name="tempcigar" value="-c" /> | |
65 <output name="output" file="5_ct.bam.expected" /> | |
66 </test> | |
67 <!-- test_cmd($opts,out=>'fixmate/5_ct.bam.expected', cmd=>"$$opts{bin}/samtools fixmate${threads} -cO sam $$opts{path}/fixmate/5_ct.sam -");--> | |
68 <test> | |
69 <param name="bamfile" value="6_ct_replace.sam" /> | |
70 <param name="tempcigar" value="-c" /> | |
71 <output name="output" file="6_ct_replace.bam.expected" /> | |
72 </test> | |
73 <!-- 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 -");--> | |
74 <test> | |
75 <param name="bamfile" value="7_two_read_mapped.sam" /> | |
76 <output name="output" file="7_two_read_mapped.bam.expected" /> | |
77 </test> | |
78 <!--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 -");--> | |
79 </tests> | |
80 <help> | |
81 **What it does** | |
82 | |
83 Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment. | |
84 </help> | |
85 <expand macro="citations"/> | |
86 </tool> |