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comparison samtools_ampliconclip.xml @ 0:a941babb9268 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_ampliconclip commit 4596e7b08744df85b48d106cf4d44ebdd90dd554
author iuc
date Mon, 27 Jun 2022 20:07:59 +0000
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children 5f3ea90dc6ae
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-1:000000000000 0:a941babb9268
1 <tool id="samtools_ampliconclip" name="Samtools ampliconclip" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>clip primer bases from bam files</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 samtools ampliconclip
12 $hard_clip_mode
13 #if $min_length:
14 --fail-len $min_length
15 #end if
16 --tolerance $tolerance
17 $strand
18 -b '${input_bed}'
19 -u
20 $both_ends
21 $no_excluded
22 -@ \$addthreads
23 '${input_bam}'
24 | samtools collate -@ \$addthreads -O -u -
25 | samtools fixmate -@ \$addthreads -u - -
26 | samtools sort -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}" -o '${output_bam}'
27 ]]></command>
28 <inputs>
29 <param name="input_bed" type="data" format="bed" label="Genetic intervals (in BED format)" />
30 <param name="input_bam" type="data" format="bam" label="BAM file" />
31 <param name="hard_clip_mode" argument="--hard-clip" type="boolean" checked="false" truevalue="--hard-clip" falsevalue="--soft-clip" label="hard clip" help="hard clip (remove bases), unchekced = default soft-clipping" />
32 <param name="strand" argument="--strand" type="boolean" checked="false" truevalue="--strand" falsevalue="" label="only clip reads that match bed file strand annotation" />
33 <param name="both_ends" argument="--both-ends" type="boolean" checked="false" truevalue="--both-ends" falsevalue="" label="clip both ends of reads (false = 5' only)" />
34 <param name="no_excluded" argument="--no-excluded" type="boolean" checked="false" truevalue="--no-excluded" falsevalue="" label="don't write excluded reads to output (default = write all)" />
35 <param name="min_length" argument="--fail-len" type="integer" min="0" optional="true" label="Min Read length" help="mark reads QCFAIL at this length or shorter after clipping" />
36 <param name="tolerance" argument="--tolerance" type="integer" value="5" min="0" label="Tolerance" help="match region within this number of bases, default 5." />
37
38 </inputs>
39 <outputs>
40 <data name="output_bam" format="bam" />
41 </outputs>
42 <tests>
43 <!-- 1) -->
44 <test>
45 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
46 <param name="input_bam" value="eboVir3.bam" ftype="bam" />
47 <output name="output_bam" file="eboVir3.clipped.bam" ftype="bam" lines_diff="22" />
48 </test>
49 <!-- 2) testing strand -->
50 <test>
51 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
52 <param name="input_bam" value="eboVir3.bam" ftype="bam" />
53 <param name="strand" value="--strand" />
54 <output name="output_bam" file="eboVir3.clipped.strand.bam" ftype="bam" lines_diff="16" />
55 </test>
56 <!-- 3) testing hard clip-->
57 <test>
58 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
59 <param name="input_bam" value="eboVir3.bam" ftype="bam" />
60 <param name="hard_clip_mode" value="--hard-clip" />
61 <output name="output_bam" file="eboVir3.hardclipped.bam" ftype="bam" lines_diff="14" />
62 </test>
63 <!-- 4) testing strand and min length-->
64 <test>
65 <param name="input_bed" value="eboVir3.1.bed" ftype="bed" />
66 <param name="input_bam" value="eboVir3.bam" ftype="bam" />
67 <param name="min_length" value="30" />
68 <param name="strand" value="--strand" />
69 <param name="tolerance" value="6" />
70 <param name="both_ends" value="--both-ends" />
71 <param name="no_excluded" value="--no-excluded" />
72 <output name="output_bam" file="eboVir3.clipped.strand_gt30.bam" ftype="bam" lines_diff="13" />
73 </test>
74
75 </tests>
76 <help>
77 **What it does**
78 Clips read alignments where they match BED file defined regions (e.g. for amplicon sequencing).
79
80 samtools ampliconclip -b [INPUT BED] [INPUT BAM1] -o [OUTPUT]
81 </help>
82 <expand macro="citations"/>
83 </tool>