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"planemo upload for repository https://github.com/tommyau/bamclipper commit 9b11f4728f3c890da7db2bba681c6fca48af43db"
author nml
date Tue, 28 Apr 2020 12:41:11 -0400
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1 <tool id="bamclipper" name="BAMClipper" version="@VERSION@+galaxy0">
2 <description> Remove gene-specific primer sequences from BAM alignments of PCR amplicons by soft-clipping with BEDPE file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 #import re
9
10 #set bamname = re.sub('[^\s\w-]', '_', str($input1.name))
11 ln -sf '$input1' '$bamname' &&
12 ln -sf '${input1.metadata.bam_index}' '${bamname}.bai' &&
13
14 bamclipper.sh -b '$bamname' -p '$primer_pairs' -n "\${GALAXY_SLOTS:-1}"
15 #if $optional.upstream:
16 -u '$optional.upstream'
17 #end if
18 #if $optional.downstream:
19 -d '$optional.downstream'
20 #end if
21
22 ]]></command>
23 <inputs>
24 <param name="input1" type="data" format="bam"
25 label="Input Bam file"
26 argument="-b"
27 />
28 <param name="primer_pairs" type="data" format="bedpe, interval"
29 label="BEDPE file of primer pair locations"
30 argument="-p"
31 />
32 <section name="optional" title="Optional Parameters" expanded="false" >
33 <param name="upstream" type="integer" optional="true"
34 label="Upstream"
35 argument="-u"
36 help="Number of nucleotides upstream of the 5' most nucleotide of the primer (in addition to 5' most nucleotide of primer) for assigning
37 alignments to primers based on the alignment starting position. Default 1"
38 />
39 <param name="downstream" type="integer" optional="true"
40 label="Downstream"
41 argument="-d"
42 help="Number of nucleotides downstream to the 5' most nucleotide of primer (in addition to 5' most nucleotide of primer) for assigning
43 alignments to primers based on the alignment starting position. Default 5"
44 />
45 </section>
46 </inputs>
47 <outputs>
48 <data format_source="input1" from_work_dir="*.primerclipped.bam" name="output" label="${input1.name}.primerclipped" />
49 </outputs>
50 <tests>
51 <test>
52 <param name="input1" value="SRR2075598.bam" />
53 <param name="primer_pairs" value="trusight_myeloid.bedpe" />
54 <output name="output" file="SRR2075598.primerclipped.bam" ftype="bam" />
55 </test>
56 <test>
57 <param name="input1" value="SRR2075598.bam" />
58 <param name="primer_pairs" value="trusight_myeloid.bedpe" />
59 <section name="optional">
60 <param name="upstream" value="1" />
61 <param name="downstream" value="5" />
62 </section>
63 <output name="output" file="SRR2075598.primerclipped.bam" ftype="bam" />
64 </test>
65 </tests>
66 <help><![CDATA[
67
68 Bamclipper
69 ----------
70
71 Soft-clip gene-specific primers from BAM alignment file based on genomic coordinates of primer pairs in BEDPE format
72 to produce a new bam file called NAME.primerclipped.bam and its associated bam index (NAME.primerclipped.bam.bai)
73
74 Example primer pair BEDPE file lines:
75
76 ::
77
78 chr1 115256390 115256417 chr1 115256622 115256650
79 chr1 115258642 115258664 chr1 115258876 115258903
80 chr10 89692737 89692767 chr10 89692971 89692998
81 chr10 89692943 89692970 chr10 89693177 89693206
82 chr10 89717567 89717596 chr10 89717775 89717802
83
84
85 ]]></help>
86 <expand macro="citations" />
87 </tool>