comparison pindel.xml @ 0:dd513c72ea56 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit 1f1c277219ca756c9baa453592b455597fd593d8-dirty
author portiahollyoak
date Tue, 17 May 2016 04:47:23 -0400
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children
comparison
equal deleted inserted replaced
-1:000000000000 0:dd513c72ea56
1 <tool id ="pindel" name="Pindel" version="0.2.5b8">
2 <description></description>
3 <requirements>
4 <requirement type="package" version="0.2.5b8">pindel</requirement>
5 </requirements>
6 <stdio>
7 <exit_code range="1:" />
8 </stdio>
9 <command><![CDATA[
10 ln -f -s "$input_file.metadata.bam_index" alignment.sorted.bam.bai &&
11 ln -f -s "$input_file" alignment.sorted.bam &&
12 ln -f -s "$reference" ref.fa &&
13 samtools faidx ref.fa &&
14 python $__tool_directory__/create_config_file.py
15 --input_file alignment.sorted.bam
16 --insert_size "$insert_size"
17 --sample_label "$input_file.element_identifier"
18 --output_config_file output_config_file &&
19 pindel
20 -f ref.fa
21 -i output_config_file
22 -c "$chromosome"
23 -o prefix &&
24 mv prefix_D $Deletions &&
25 mv prefix_SI $Short_Insertions &&
26 mv prefix_LI $Long_Insertions &&
27 mv prefix_INV $Inversions &&
28 mv prefix_TD $Tandem_Duplications &&
29 mv prefix_RP $Read_Pair &&
30 mv prefix_INT_final $INT_final &&
31 mv prefix_CloseEndMapped $Close_End_Mapped
32 ]]></command>
33 <inputs>
34 <param format="bam" name="input_file" type="data" label="One or more BAM alignment files produced by BWA"/>
35 <param name="insert_size" type="integer" value="" label="Expected Insert size" />
36 <param format="fasta" name="reference" type="data" label="Reference genome in fasta format"/>
37 <param name="chromosome" type="text" value="ALL" help="Select a chromsome. ALL will use all chromosomes"
38 label="Which chromosome to operate on"/>
39 </inputs>
40 <outputs>
41 <data format="txt" name="Deletions" type="data" label="${input_file.element_identifier} Deletions"/>
42 <data format="txt" name="Short_Insertions" type="data" label="${input_file.element_identifier} Short Insertions"/>
43 <data format="txt" name="Long_Insertions" type="data" label="${input_file.element_identifier} Long Insertions"/>
44 <data format="txt" name="Inversions" type="data" label="${input_file.element_identifier} Inversions"/>
45 <data format="txt" name="Tandem_Duplications" type="data" label="${input_file.element_identifier} Tandom Duplications"/>
46 <data format="txt" name="Breakpoints" type="data" label="${input_file.element_identifier} Breakpoints"/>
47 <data format="txt" name="Read_Pair" type="data" label="${input_file.element_identifier} Read Pair Evidence"/>
48 <data format="txt" name="INT_final" type="data" label="${input_file.element_identifier} INT_final"/>
49 <data format="txt" name="Close_End_Mapped" type="data" label="${input_file.element_identifier} Close End Mapped"/>
50 </outputs>
51 <tests>
52 <test>
53 <param name="input_file" value="X_100000_Hum1.bam" ftype="bam"/>
54 <param name="insert_size" value="250"/>
55 <param name="reference" value="dm6.fa" ftype="fasta"/>
56 <param name="chromosome" value="ALL"/>
57 <output name="Deletions" file="X_100000_Hum1.bam_Deletions" ftype="txt"/>
58 <output name="Short_Insertions" file="X_100000_Hum1.bam_Short_Insertions" ftype="txt"/>
59 <output name="Long_Insertions" file="X_100000_Hum1.bam_Long_Insertions" ftype="txt"/>
60 <output name="Inversions" file="X_100000_Hum1.bam_Inversions" ftype="txt"/>
61 <output name="Tandem_Duplications" file="X_100000_Hum1.bam_Tandem_Duplications" ftype="txt"/>
62 <output name="Breakpoints" file="X_100000_Hum1.bam_Breakpoints" ftype="txt"/>
63 <output name="Read_Pair" file="X_100000_Hum1.bam_Read_Pair_Evidence" ftype="txt"/>
64 <output name="INT_Final" file="X_100000_Hum1.bam_INT_final" ftype="txt"/>
65 <output name="Close_End_Mapped" file="X_100000_Hum1.bam_Close_End_Mapped" ftype="txt"/>
66 </test>
67 </tests>
68 <help> <![CDATA[
69
70 Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-generation sequencing data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
71
72 The following inputs/parameters are required:
73 - One or more BAM alignment files produced by BWA
74 - Expected Insert Size for each alignment file
75 - Sample label for each alignment file
76 - Reference genome in fasta format (same one used in alignment)
77 - Which chromosome to operate on
78
79 The following output files are produced by Pindel:
80 - Deletions
81 - Short Insertions
82 - Long Insertions
83 - Inversions
84 - Tandom Duplications
85 - Breakpoints
86 - Read Pair Evidence
87 - INT_final
88 - Close End Mapped
89
90 ]]> </help>
91 <citations>
92 <citation type="doi">doi:10.1093/bioinformatics/btp394</citation>
93 </citations>
94 </tool>