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comparison samtools_fixmate.xml @ 1:595ae1ba934a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_fixmate commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
author iuc
date Tue, 28 Sep 2021 16:13:23 +0000
parents bc0cc7bfbfe9
children 41e36c99a008
comparison
equal deleted inserted replaced
0:bc0cc7bfbfe9 1:595ae1ba934a
1 <tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@"> 1 <tool id="samtools_fixmate" name="Samtools fixmate" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>fill mate coordinates, ISIZE and mate related flags</description> 2 <description>fill mate coordinates, ISIZE and mate related flags</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @ADDTHREADS@ 10 @ADDTHREADS@
11 ## name sort input 11 ## name sort input
12 #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'): 12 #if not $bamfile.is_of_type('qname_sorted.bam', 'qnamed_input_sorted.bam'):
13 samtools sort 13 samtools sort
14 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp 14 -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
15 -n 15 -n
16 -O BAM 16 -O BAM
17 -o namesorted.bam 17 -o namesorted.bam
18 '$bamfile' && 18 '$bamfile' &&
19 #else: 19 #else:
20 ln -s '$bamfile' namesorted.bam && 20 ln -s '$bamfile' namesorted.bam &&
36 <param name="noprop" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Disable FR proper pair check" /> 36 <param name="noprop" type="boolean" argument="-p" truevalue="-p" falsevalue="" checked="false" label="Disable FR proper pair check" />
37 <param name="tempcigar" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Add template cigar ct tag" /> 37 <param name="tempcigar" type="boolean" argument="-c" truevalue="-c" falsevalue="" checked="false" label="Add template cigar ct tag" />
38 <param name="addms" type="boolean" argument="-m" truevalue="-m" falsevalue="" checked="false" label="Add ms (mate score) tags" help="These are used by markdup to select the best reads to keep." /> 38 <param name="addms" type="boolean" argument="-m" truevalue="-m" falsevalue="" checked="false" label="Add ms (mate score) tags" help="These are used by markdup to select the best reads to keep." />
39 </inputs> 39 </inputs>
40 <outputs> 40 <outputs>
41 <!--<data name="output" format="sam" />--> 41 <!--<data name="output" format="sam" />-->
42 <data name="output" format="qname_sorted.bam"/> 42 <data name="output" format="qname_sorted.bam"/>
43 </outputs> 43 </outputs>
44 <tests> 44 <tests>
45 <!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493--> 45 <!-- from https://github.com/samtools/samtools/blob/6d79411685d8f0fbb34e123f52d72b63271f4dcb/test/test.pl#L2493-->
46 <!-- test_cmd($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);--> 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> 47 <test>
48 <param name="bamfile" value="2_isize_overflow.sam" /> 48 <param name="bamfile" value="2_isize_overflow.sam" ftype="sam" />
49 <output name="output" file="2_isize_overflow.bam.expected" /> 49 <output name="output" file="2_isize_overflow.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
50 </test> 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 -");--> 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> 52 <test>
53 <param name="bamfile" value="3_reverse_read_pp_lt.sam" /> 53 <param name="bamfile" value="3_reverse_read_pp_lt.sam" ftype="sam" />
54 <output name="output" file="3_reverse_read_pp_lt.bam.expected" /> 54 <output name="output" file="3_reverse_read_pp_lt.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
55 </test> 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 -");--> 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> 57 <test>
58 <param name="bamfile" value="4_reverse_read_pp_equal.sam" /> 58 <param name="bamfile" value="4_reverse_read_pp_equal.sam" ftype="sam" />
59 <output name="output" file="4_reverse_read_pp_equal.bam.expected" /> 59 <output name="output" file="4_reverse_read_pp_equal.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
60 </test> 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 -");--> 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> 62 <test>
63 <param name="bamfile" value="5_ct.sam" /> 63 <param name="bamfile" value="5_ct.sam" ftype="sam" />
64 <param name="tempcigar" value="-c" /> 64 <param name="tempcigar" value="-c" />
65 <output name="output" file="5_ct.bam.expected" /> 65 <output name="output" file="5_ct.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
66 </test> 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 -");--> 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> 68 <test>
69 <param name="bamfile" value="6_ct_replace.sam" /> 69 <param name="bamfile" value="6_ct_replace.sam" ftype="sam" />
70 <param name="tempcigar" value="-c" /> 70 <param name="tempcigar" value="-c" />
71 <output name="output" file="6_ct_replace.bam.expected" /> 71 <output name="output" file="6_ct_replace.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
72 </test> 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 -");--> 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> 74 <test>
75 <param name="bamfile" value="7_two_read_mapped.sam" /> 75 <param name="bamfile" value="7_two_read_mapped.sam" ftype="sam" />
76 <output name="output" file="7_two_read_mapped.bam.expected" /> 76 <output name="output" file="7_two_read_mapped.bam.expected" ftype="qname_sorted.bam" lines_diff="4" />
77 </test> 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 -");--> 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> 79 </tests>
80 <help> 80 <help>
81 **What it does** 81 **What it does**
82 82
83 Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment. 83 Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment.