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comparison igvtools_sort.xml @ 0:2eb1e2924c1a

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author jjohnson
date Tue, 17 Jan 2012 21:53:25 -0500
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1 <tool id="igvtools_sort" name="IGVtools sort" version="1.0">
2 <description>input file by start position</description>
3 <command interpreter="bash">igvtools sort -t .
4 ## IGVTools relies on the file extension to determine format
5 #if $input.datatype.file_ext == 'vcf':
6 #set $input_name='input_file.vcf'
7 #set $output_name='output.vcf'
8 #elif $input.datatype.file_ext == 'sam':
9 #set $input_name='input_file.sam'
10 #set $output_name='output.sam'
11 #elif $input.datatype.file_ext == 'bed':
12 #set $input_name='input_file.bed'
13 #set $output_name='output.bed'
14 #elif $input.datatype.file_ext == 'psl':
15 #set $input_name='input_file.psl'
16 #set $output_name='output.psl'
17 #elif $input.datatype.file_ext == 'igv':
18 #set $input_name='input_file.igv'
19 #set $output_name='output.igv'
20 #elif $input.datatype.file_ext == 'igv.cn':
21 #set $input_name='input_file.cn'
22 #set $output_name='output.cn'
23 #end if
24 `ln -s $input $input_name; echo $input_name` $output_name
25 </command>
26 <inputs>
27 <param name="input" type="data" format="sam,bed,vcf,psl,igv,igv.cn," label="Input file SAM,BED,VCF format"
28 help="Use samtools or picard to sort bam files"/>
29 </inputs>
30 <outputs>
31 <data format_source="input" name="output_sam" metadata_source="input" label="${tool.name} on ${on_string}: igv.sam" from_work_dir="output.sam">
32 <filter>(input.datatype.file_ext == 'sam')</filter>
33 </data>
34 <data format_source="input" name="output_bed" metadata_source="input" label="${tool.name} on ${on_string}: igv.bed" from_work_dir="output.bed">
35 <filter>(input.datatype.file_ext == 'bed')</filter>
36 </data>
37 <data format_source="input" name="output_vcf" metadata_source="input" label="${tool.name} on ${on_string}: igv.vcf" from_work_dir="output.vcf">
38 <filter>(input.datatype.file_ext == 'vcf')</filter>
39 </data>
40 <data format_source="input" name="output_psl" metadata_source="input" label="${tool.name} on ${on_string}: igv.vcf" from_work_dir="output.psl">
41 <filter>(input.datatype.file_ext == 'psl')</filter>
42 </data>
43 <data format_source="input" name="output_igv" metadata_source="input" label="${tool.name} on ${on_string}: igv" from_work_dir="output.igv">
44 <filter>(input.datatype.file_ext == 'igv')</filter>
45 </data>
46 <data format_source="input" name="output_cn" metadata_source="input" label="${tool.name} on ${on_string}: igv.cn" from_work_dir="output.cn">
47 <filter>(input.datatype.file_ext == 'igv.cn')</filter>
48 </data>
49 </outputs>
50 <tests>
51 </tests>
52 <help>
53 **What it does**
54
55 The IGVTools_ sort command sorts the input file by start position, as required.
56
57 .. _IGVTools: http://www.broadinstitute.org/software/igv/igvtools_commandline
58 .. _IGV: http://www.broadinstitute.org/igv/
59
60 ------
61
62 To cite your use of IGV in your publication::
63
64 James T. Robinson, Helga Thorvaldsdottir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz, Jill P. Mesirov.
65 Integrative Genomics Viewer. Nature Biotechnology 29, 24-26 (2011)
66
67 ------
68
69 **Input formats**
70
71 Supported input file formats are: .cn, .igv, .sam, .aligned, .psl, .bed, and .vcf.
72
73 ------
74
75 **Outputs**
76
77 The output will have the same format as the input file.
78
79 </help>
80 </tool>