Mercurial > repos > artbio > sr_bowtie
changeset 2:304adcfe3660 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 9700ca1c08ed2cfbca33630892569f3b8acec6fe
| author | artbio |
|---|---|
| date | Wed, 31 Jan 2018 17:55:20 -0500 |
| parents | 5f4fbba31b6a |
| children | 61ab0d4bd187 |
| files | sRbowtie.xml test-data/input.fastqsanger |
| diffstat | 2 files changed, 32 insertions(+), 3 deletions(-) [+] |
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--- a/sRbowtie.xml Wed Oct 11 06:01:15 2017 -0400 +++ b/sRbowtie.xml Wed Jan 31 17:55:20 2018 -0500 @@ -1,7 +1,7 @@ -<tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.1"> +<tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.2"> <description>for small RNA short reads</description> <requirements> - <requirement type="package" version="1.1.2=py27_2">bowtie</requirement> + <requirement type="package" version="1.1.2=py27_0">bowtie</requirement> <requirement type="package" version="1.2">samtools</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ @@ -14,7 +14,7 @@ #end if #if $input.extension == "fasta": #set format = "-f" - #elif $input.extension == "fastq": + #elif $input.extension == "fastq" or $input.extension == "fastqsanger": #set format = "-q" #end if @@ -153,6 +153,15 @@ <test> <param name="genomeSource" value="history" /> <param ftype="fasta" name="ownFile" value="297_reference.fa" /> + <param name="method" value="unique" /> + <param ftype="fastqsanger" name="input" value="input.fastqsanger" /> + <param name="v_mismatches" value="1" /> + <param name="output_format" value="bam" /> + <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> + </test> + <test> + <param name="genomeSource" value="history" /> + <param ftype="fasta" name="ownFile" value="297_reference.fa" /> <param name="method" value="multiple" /> <param ftype="fasta" name="input" value="input.fa" /> <param name="v_mismatches" value="1" />
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fastqsanger Wed Jan 31 17:55:20 2018 -0500 @@ -0,0 +1,20 @@ +@HTW-1 +CATTCTGCGAAGAAGC ++ +HHHHHHHHHHHHHHHH +@HTW-2 +GGAGAGACGACGTCAATTACT ++ +HHHHHHHHHHHHHHHHHHHHH +@HTW-3 +AATTTCGAAACTACACCTGGAAGGTAACCA ++ +HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH +@HTW-4 +ATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT ++ +HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH +@HTW-5 +TAAGATACTGATAAGGAAACTACCAATA ++ +HHHHHHHHHHHHHHHHHHHHHHHHHHHH