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comparison samtools_fixmate.xml @ 0:47c0cf039aae draft

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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 04:28:03 -0400
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children 77af4d28aca3
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-1:000000000000 0:47c0cf039aae
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>