Mercurial > repos > artbio > pindel
comparison pindelwrapper.xml @ 0:decc6b5631dc draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/pindel commit 9bae2cc35b71dabcb73cd586eb1bdc458132548c"
author | artbio |
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date | Wed, 29 Sep 2021 21:30:31 +0000 |
parents | |
children | 078c6ab38858 |
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1 <tool id ="pindel" name="Pindel" version="0.2.5b8+galaxy1"> | |
2 <description></description> | |
3 <requirements> | |
4 <requirement type="package" version="0.2.5b8">pindel</requirement> | |
5 <requirement type="package" version="1.0">openssl</requirement> | |
6 <requirement type="package" version="1.7">samtools</requirement> | |
7 <requirement type="package" version="3.7">python</requirement> | |
8 </requirements> | |
9 <stdio> | |
10 <exit_code range="1:" /> | |
11 </stdio> | |
12 <command><![CDATA[ | |
13 ln -f -s "$input_file.metadata.bam_index" alignment.sorted.bam.bai && | |
14 ln -f -s "$input_file" alignment.sorted.bam && | |
15 ln -f -s "$reference" ref.fa && | |
16 samtools faidx ref.fa && | |
17 python $__tool_directory__/create_config_file.py | |
18 --input_file alignment.sorted.bam | |
19 --insert_size "$insert_size" | |
20 --sample_label "$input_file.element_identifier" | |
21 --output_config_file output_config_file && | |
22 pindel | |
23 -f ref.fa | |
24 -i output_config_file | |
25 -c "$chromosome" | |
26 -o prefix && | |
27 mv prefix_D $Deletions && | |
28 mv prefix_SI $Short_Insertions && | |
29 mv prefix_LI $Long_Insertions && | |
30 mv prefix_INV $Inversions && | |
31 mv prefix_TD $Tandem_Duplications && | |
32 mv prefix_RP $Read_Pair && | |
33 mv prefix_INT_final $int_final && | |
34 mv prefix_CloseEndMapped $Close_End_Mapped | |
35 ]]></command> | |
36 <inputs> | |
37 <param format="bam" name="input_file" type="data" label="One or more BAM alignment files produced by BWA"/> | |
38 <param name="insert_size" type="integer" value="" label="Expected Insert size" /> | |
39 <param format="fasta" name="reference" type="data" label="Reference genome in fasta format"/> | |
40 <param name="chromosome" type="text" value="ALL" help="Select a chromsome. ALL will use all chromosomes" | |
41 label="Which chromosome to operate on"/> | |
42 </inputs> | |
43 <outputs> | |
44 <data format="txt" name="Deletions" label="${input_file.element_identifier} Deletions"/> | |
45 <data format="txt" name="Short_Insertions" label="${input_file.element_identifier} Short Insertions"/> | |
46 <data format="txt" name="Long_Insertions" label="${input_file.element_identifier} Long Insertions"/> | |
47 <data format="txt" name="Inversions" label="${input_file.element_identifier} Inversions"/> | |
48 <data format="txt" name="Tandem_Duplications" label="${input_file.element_identifier} Tandem Duplications"/> | |
49 <data format="txt" name="Breakpoints" label="${input_file.element_identifier} Breakpoints"/> | |
50 <data format="txt" name="Read_Pair" label="${input_file.element_identifier} Read Pair Evidence"/> | |
51 <data format="txt" name="int_final" label="${input_file.element_identifier} INT_final"/> | |
52 <data format="txt" name="Close_End_Mapped" label="${input_file.element_identifier} Close End Mapped"/> | |
53 </outputs> | |
54 <tests> | |
55 <test> | |
56 <param name="input_file" value="X_100000_Hum1.bam" ftype="bam"/> | |
57 <param name="insert_size" value="250"/> | |
58 <param name="reference" value="dm6_X.fasta" ftype="fasta"/> | |
59 <param name="chromosome" value="ALL"/> | |
60 <output name="Deletions" file="X_100000_Hum1.bam_Deletions.txt" ftype="txt"/> | |
61 <output name="Short_Insertions" file="X_100000_Hum1.bam_Short_Insertions.txt" ftype="txt"/> | |
62 <output name="Long_Insertions" file="X_100000_Hum1.bam_Long_Insertions.txt" ftype="txt"/> | |
63 <output name="Inversions" file="X_100000_Hum1.bam_Inversions.txt" ftype="txt"/> | |
64 <output name="Tandem_Duplications" file="X_100000_Hum1.bam_Tandem_Duplications.txt" ftype="txt"/> | |
65 <output name="Breakpoints" file="X_100000_Hum1.bam_Breakpoints.txt" ftype="txt"/> | |
66 <output name="Read_Pair" file="X_100000_Hum1.bam_Read_Pair_Evidence.txt" ftype="txt"/> | |
67 <output name="int_final" file="X_100000_Hum1.bam_INT_final.txt" ftype="txt"/> | |
68 <output name="Close_End_Mapped" file="X_100000_Hum1.bam_Close_End_Mapped.txt" ftype="txt"/> | |
69 </test> | |
70 </tests> | |
71 <help> <![CDATA[ | |
72 | |
73 Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, | |
74 tandem duplications and other structural variants at single-based resolution from | |
75 next-generation sequencing data. It uses a pattern growth approach to identify the | |
76 breakpoints of these variants from paired-end short reads. | |
77 | |
78 The following inputs/parameters are required: | |
79 - One or more BAM alignment files produced by BWA | |
80 - Expected Insert Size for each alignment file | |
81 - Sample label for each alignment file | |
82 - Reference genome in fasta format (the same one used in alignment) | |
83 - Which chromosome to operate on | |
84 | |
85 The following output files are produced by Pindel: | |
86 - Deletions | |
87 - Short Insertions | |
88 - Long Insertions | |
89 - Inversions | |
90 - Tandom Duplications | |
91 - Breakpoints | |
92 - Read Pair Evidence | |
93 - INT_final | |
94 - Close End Mapped | |
95 | |
96 | |
97 ]]> </help> | |
98 <citations> | |
99 <citation type="doi">doi:10.1093/bioinformatics/btp394</citation> | |
100 </citations> | |
101 </tool> |