Mercurial > repos > chrisd > snipfinder
comparison variant_caller.xml @ 1:d612ce3827b9 draft
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/snpfinder commit 60b005a83eab4984bc88a85a07ca2e416c3e507c-dirty
| author | chrisd |
|---|---|
| date | Thu, 30 Jun 2016 02:39:23 -0400 |
| parents | d9be5a7e70f5 |
| children |
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| 0:d9be5a7e70f5 | 1:d612ce3827b9 |
|---|---|
| 6 <stdio> | 6 <stdio> |
| 7 <exit_code range="1:" /> | 7 <exit_code range="1:" /> |
| 8 </stdio> | 8 </stdio> |
| 9 <command><![CDATA[ | 9 <command><![CDATA[ |
| 10 snp | 10 snp |
| 11 -amr_fp $input1 | 11 -amr_fp $reference |
| 12 #if $sam_type.mode == "single_end" | 12 #if $sam_type.mode == "single_end" |
| 13 -samse $sam_type.samse_input2 | 13 -samse $sam_type.samse_input |
| 14 $sam_type.best | 14 $sam_type.best |
| 15 #else | 15 #else |
| 16 -sampe $sam_type.sampe_input2 | 16 -sampe $sam_type.sampe_input |
| 17 $sam_type.best | 17 $sam_type.best |
| 18 #end if | 18 #end if |
| 19 -out_fp $output1 | 19 -out_fp $result |
| 20 ]]></command> | 20 ]]></command> |
| 21 <inputs> | 21 <inputs> |
| 22 <param type="data" name="input1" format="fasta" label="Reference sequence"/> | 22 <param type="data" name="reference" format="fasta" label="Reference sequence"/> |
| 23 <conditional name="sam_type"> | 23 <conditional name="sam_type"> |
| 24 <param name="mode" type="select" label="SAM file type"> | 24 <param name="mode" type="select" label="SAM file type"> |
| 25 <option value="single_end"></option> | 25 <option value="single_end"></option> |
| 26 <option value="paired_end"></option> | 26 <option value="paired_end"></option> |
| 27 </param> | 27 </param> |
| 28 <when value="single_end"> | 28 <when value="single_end"> |
| 29 <param type="data" name="samse_input2" format="sam" label="Single-end SAM file"/> | 29 <param type="data" name="samse_input" format="sam" label="Single-end SAM file"/> |
| 30 <param name="best" type="boolean" label="Filter on unique alignments" | 30 <param name="best" type="boolean" label="Filter on unique alignments" truevalue="-b" falsevalue=""/> |
| 31 truevalue="-b" falsevalue="" /> | |
| 32 </when> | 31 </when> |
| 33 <when value="paired_end"> | 32 <when value="paired_end"> |
| 34 <param type="data" name="sampe_input2" format="sam" label="Paired-end SAM file"/> | 33 <param type="data" name="sampe_input" format="sam" label="Paired-end SAM file"/> |
| 35 <param name="best" type="boolean" label="Filter on unique alignments" | 34 <param name="best" type="boolean" label="Filter on unique alignments" truevalue="-b" falsevalue=""/> |
| 36 truevalue="-b" falsevalue="" /> | |
| 37 </when> | 35 </when> |
| 38 </conditional> | 36 </conditional> |
| 39 </inputs> | 37 </inputs> |
| 40 <outputs> | 38 <outputs> |
| 41 <data name="output1" format="tabular" /> | 39 <data name="result" format="tabular" /> |
| 42 </outputs> | 40 </outputs> |
| 43 <tests> | 41 <tests> |
| 44 <test> | 42 <test> |
| 45 <param name="input1" value="ref.fa"/> | 43 <param name="mode" value="single_end"/> |
| 46 <param name="sam_type.samse_input2" value="samse.sam"/> | 44 <param name="reference" value="ref.fa"/> |
| 47 <output name="output1" value="samse_result"/> | 45 <param name="samse_input" value="samse.sam"/> |
| 46 <output name="result" file="samse_result" ftype="tabular"/> | |
| 48 </test> | 47 </test> |
| 49 <test> | 48 <test> |
| 50 <param name="input1" value="ref.fa"/> | 49 <param name="mode" value="paired_end"/> |
| 51 <param name="sam_type.sampe_input2" value="sampe.sam"/> | 50 <param name="reference" value="ref.fa"/> |
| 52 <output name="output1" value="sampe_result"/> | 51 <param name="sampe_input" value="sampe.sam"/> |
| 53 </test> | 52 <output name="result" file="sampe_result" ftype="tabular"/> |
| 53 </test> | |
| 54 </tests> | 54 </tests> |
| 55 <help><![CDATA[ | 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. | 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 | 57 |
| 58 Program: snpfinder | 58 Program: snpfinder |