mirror of
https://github.com/galaxyproject/galaxy.git
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Kelly Vincent
f61d147034
Made Bowtie test files longer (more than one test read). Added explanation of canonical and full reference genome variants to BWA and Bowtie. Added informative labels to output files for NGS tools.
70 lines
2.6 KiB
XML
70 lines
2.6 KiB
XML
<tool id="sam2interval" name="Convert SAM" version="1.0.1">
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<description>to interval</description>
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<command interpreter="python">sam2interval.py --input_sam_file=$input1 $print_all > $out_file1
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</command>
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<inputs>
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<param format="sam" name="input1" type="data" label="Select dataset to convert"/>
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<param name="print_all" type="select" label="Print all?" help="Do you want to retain original SAM fields? See example below.">
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<option value="-p">Yes</option>
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<option value="">No</option>
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</param>
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</inputs>
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<outputs>
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<data format="interval" name="out_file1" label="Converted Interval" />
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</outputs>
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<tests>
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<test>
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<param name="input1" value="sam_bioinf_example.sam" ftype="sam"/>
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<param name="flags" value="Read is mapped in a proper pair"/>
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<param name="print_all" value="Yes"/>
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<output name="out_file1" file="sam2interval_printAll.dat" ftype="interval"/>
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</test>
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<test>
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<param name="input1" value="sam_bioinf_example.sam" ftype="sam"/>
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<param name="flags" value="Read is mapped in a proper pair"/>
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<param name="print_all" value="No"/>
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<output name="out_file1" file="sam2interval_noprintAll.dat" ftype="interval"/>
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</test>
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</tests>
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<help>
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**What it does**
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Converts positional information from a SAM dataset into interval format with 0-based start and 1-based end. CIGAR string of SAM format is used to compute the end coordinate.
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-----
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**Example**
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Converting the following dataset::
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r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA *
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r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA *
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r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1
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r004 0 ref 16 30 6M14N5M * 0 0 ATAGCTTCAGC *
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r003 16 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0
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r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT *
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into Interval format will produce the following if *Print all?* is set to **Yes**::
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ref 6 22 + r001 163 ref 7 30 8M2I4M1D3M = 37 39 TTAGATAAAGGATACTA *
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ref 8 19 + r002 0 ref 9 30 3S6M1P1I4M * 0 0 AAAAGATAAGGATA *
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ref 8 14 + r003 0 ref 9 30 5H6M * 0 0 AGCTAA * NM:i:1
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ref 15 40 + r004 0 ref 16 30 6M14N5M * 0 0 ATAGCTTCAGC *
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ref 28 33 - r003 16 ref 29 30 6H5M * 0 0 TAGGC * NM:i:0
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ref 36 45 - r001 83 ref 37 30 9M = 7 -39 CAGCGCCAT *
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Setting *Print all?* to **No** will generate the following::
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ref 6 22 + r001
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ref 8 19 + r002
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ref 8 14 + r003
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ref 15 40 + r004
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ref 28 33 - r003
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ref 36 45 - r001
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</help>
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</tool>
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