Mercurial > repos > chrisd > snipfinder
comparison variant_caller.xml @ 0:d9be5a7e70f5 draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/snpfinder commit 8b7c17352f46ab4fce3bc13c3e63d4021fe83ae7
| author | chrisd |
|---|---|
| date | Wed, 23 Mar 2016 18:04:21 -0400 |
| parents | |
| children | d612ce3827b9 |
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| -1:000000000000 | 0:d9be5a7e70f5 |
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| 1 <tool id="snp_caller" name="Snip Finder" version="0.1.0"> | |
| 2 <description>Identifies snips for both single-end and paired-end data</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="0.1">snp_caller</requirement> | |
| 5 </requirements> | |
| 6 <stdio> | |
| 7 <exit_code range="1:" /> | |
| 8 </stdio> | |
| 9 <command><![CDATA[ | |
| 10 snp | |
| 11 -amr_fp $input1 | |
| 12 #if $sam_type.mode == "single_end" | |
| 13 -samse $sam_type.samse_input2 | |
| 14 $sam_type.best | |
| 15 #else | |
| 16 -sampe $sam_type.sampe_input2 | |
| 17 $sam_type.best | |
| 18 #end if | |
| 19 -out_fp $output1 | |
| 20 ]]></command> | |
| 21 <inputs> | |
| 22 <param type="data" name="input1" format="fasta" label="Reference sequence"/> | |
| 23 <conditional name="sam_type"> | |
| 24 <param name="mode" type="select" label="SAM file type"> | |
| 25 <option value="single_end"></option> | |
| 26 <option value="paired_end"></option> | |
| 27 </param> | |
| 28 <when value="single_end"> | |
| 29 <param type="data" name="samse_input2" format="sam" label="Single-end SAM file"/> | |
| 30 <param name="best" type="boolean" label="Filter on unique alignments" | |
| 31 truevalue="-b" falsevalue="" /> | |
| 32 </when> | |
| 33 <when value="paired_end"> | |
| 34 <param type="data" name="sampe_input2" format="sam" label="Paired-end SAM file"/> | |
| 35 <param name="best" type="boolean" label="Filter on unique alignments" | |
| 36 truevalue="-b" falsevalue="" /> | |
| 37 </when> | |
| 38 </conditional> | |
| 39 </inputs> | |
| 40 <outputs> | |
| 41 <data name="output1" format="tabular" /> | |
| 42 </outputs> | |
| 43 <tests> | |
| 44 <test> | |
| 45 <param name="input1" value="ref.fa"/> | |
| 46 <param name="sam_type.samse_input2" value="samse.sam"/> | |
| 47 <output name="output1" value="samse_result"/> | |
| 48 </test> | |
| 49 <test> | |
| 50 <param name="input1" value="ref.fa"/> | |
| 51 <param name="sam_type.sampe_input2" value="sampe.sam"/> | |
| 52 <output name="output1" value="sampe_result"/> | |
| 53 </test> | |
| 54 </tests> | |
| 55 <help><![CDATA[ | |
| 56 This program parses a SAM file and looks for single nucleotide polymorphisms (SNPs). In single-end mode, only alignments with bit four not set are considered. In paired-end mode, only reads that mapped in a proper pair are considered. When filtering on unique alignments, only alignments with the XT:A:U field are considered. | |
| 57 | |
| 58 Program: snpfinder | |
| 59 | |
| 60 Contact: Chris Dean <cdean11@rams.colostate.edu> | |
| 61 | |
| 62 Usage: snp [options] | |
| 63 | |
| 64 Options: | |
| 65 -amr_fp amr database path | |
| 66 -samse single-end sam file path | |
| 67 -sampe paired-end sam file path | |
| 68 -b filter on unique alignments | |
| 69 ]]></help> | |
| 70 <citations> | |
| 71 </citations> | |
| 72 </tool> |