Mercurial > repos > chrisd > snipfinder
changeset 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 | c5085b1ad596 |
| files | test-data/sampe_result test-data/samse_best_result test-data/samse_result variant_caller.xml |
| diffstat | 4 files changed, 24 insertions(+), 23 deletions(-) [+] |
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--- a/test-data/sampe_result Wed Mar 23 18:04:21 2016 -0400 +++ b/test-data/sampe_result Thu Jun 30 02:39:23 2016 -0400 @@ -1,4 +1,4 @@ -Chr,Haplotype,Frequency +Gene,Haplotype Pattern,Occurrence chr2:172936693-172938111,1052T->G:1084C->A:1102G->C:,1 chr2:172936693-172938111,119A->C:126A->C:466T->G:496A->T:,1 chr2:172936693-172938111,135A->C:138C->G:,1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samse_best_result Thu Jun 30 02:39:23 2016 -0400 @@ -0,0 +1,1 @@ +Gene,Haplotype Pattern,Occurrence
--- a/test-data/samse_result Wed Mar 23 18:04:21 2016 -0400 +++ b/test-data/samse_result Thu Jun 30 02:39:23 2016 -0400 @@ -1,4 +1,4 @@ -Chr,Haplotype,Frequency +Gene,Haplotype Pattern,Occurrence chr2:172936693-172938111,1181C->A:1190G->C:,1 chr2:172936693-172938111,1263T->G:1304A->T:1309A->T:,1 chr2:172936693-172938111,213T->A:242T->A:257T->A:,1
--- a/variant_caller.xml Wed Mar 23 18:04:21 2016 -0400 +++ b/variant_caller.xml Thu Jun 30 02:39:23 2016 -0400 @@ -8,49 +8,49 @@ </stdio> <command><![CDATA[ snp - -amr_fp $input1 + -amr_fp $reference #if $sam_type.mode == "single_end" - -samse $sam_type.samse_input2 + -samse $sam_type.samse_input $sam_type.best #else - -sampe $sam_type.sampe_input2 + -sampe $sam_type.sampe_input $sam_type.best #end if - -out_fp $output1 + -out_fp $result ]]></command> <inputs> - <param type="data" name="input1" format="fasta" label="Reference sequence"/> + <param type="data" name="reference" format="fasta" label="Reference sequence"/> <conditional name="sam_type"> <param name="mode" type="select" label="SAM file type"> <option value="single_end"></option> <option value="paired_end"></option> </param> <when value="single_end"> - <param type="data" name="samse_input2" format="sam" label="Single-end SAM file"/> - <param name="best" type="boolean" label="Filter on unique alignments" - truevalue="-b" falsevalue="" /> + <param type="data" name="samse_input" format="sam" label="Single-end SAM file"/> + <param name="best" type="boolean" label="Filter on unique alignments" truevalue="-b" falsevalue=""/> </when> <when value="paired_end"> - <param type="data" name="sampe_input2" format="sam" label="Paired-end SAM file"/> - <param name="best" type="boolean" label="Filter on unique alignments" - truevalue="-b" falsevalue="" /> + <param type="data" name="sampe_input" format="sam" label="Paired-end SAM file"/> + <param name="best" type="boolean" label="Filter on unique alignments" truevalue="-b" falsevalue=""/> </when> </conditional> </inputs> <outputs> - <data name="output1" format="tabular" /> + <data name="result" format="tabular" /> </outputs> <tests> - <test> - <param name="input1" value="ref.fa"/> - <param name="sam_type.samse_input2" value="samse.sam"/> - <output name="output1" value="samse_result"/> + <test> + <param name="mode" value="single_end"/> + <param name="reference" value="ref.fa"/> + <param name="samse_input" value="samse.sam"/> + <output name="result" file="samse_result" ftype="tabular"/> </test> - <test> - <param name="input1" value="ref.fa"/> - <param name="sam_type.sampe_input2" value="sampe.sam"/> - <output name="output1" value="sampe_result"/> - </test> + <test> + <param name="mode" value="paired_end"/> + <param name="reference" value="ref.fa"/> + <param name="sampe_input" value="sampe.sam"/> + <output name="result" file="sampe_result" ftype="tabular"/> + </test> </tests> <help><![CDATA[ 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.