Mercurial > repos > drosofff > msp_sr_bowtie
changeset 27:2578aea69626 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_sr_bowtie commit 65a33cc7068479ceeb6cdb371de557af475b9c86
author | drosofff |
---|---|
date | Sun, 02 Jul 2017 07:15:35 -0400 |
parents | 405cd77e5a83 |
children | c1ae0c9ad7d1 |
files | sRbowtie.xml test-data/al.fa test-data/output.tab |
diffstat | 3 files changed, 39 insertions(+), 4 deletions(-) [+] |
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--- a/sRbowtie.xml Fri Jun 30 18:46:35 2017 -0400 +++ b/sRbowtie.xml Sun Jul 02 07:15:35 2017 -0400 @@ -46,13 +46,13 @@ ## run the bowtie alignement #if str($output_format) == "tabular": - bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' --suppress 6,7,8 '$extra_output' local_index '$format' '$input' > '$output' + bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 local_index $format '$input' > '$output' #elif str($output_format) == "sam": - bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input > $output + bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' > '$output' #elif str($output_format) == "bam": - bowtie -p \${GALAXY_SLOTS:-4} '$method_postfix' '$extra_output' -S local_index '$format' $input | samtools view -uS | samtools sort -O bam -o '$output' + bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S local_index $format '$input' | samtools sort -O bam -o '$output' #end if - + ##### | samtools view -uS ]]></command> <inputs> <param format="fasta, fastq" help="Only with clipped, raw fasta files" label="Input fasta file: reads clipped from their adapter" name="input" type="data" /> @@ -148,6 +148,26 @@ <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" /> + <param name="output_format" value="tabular" /> + <output file="output.tab" ftype="tabular" 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" /> + <param name="additional_fasta" value="al" /> + <param name="output_format" value="tabular" /> + <output file="output.tab" ftype="tabular" name="output" /> + <output file="al.fa" ftype="fasta" name="aligned" /> + </test> </tests> <help>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/al.fa Sun Jul 02 07:15:35 2017 -0400 @@ -0,0 +1,10 @@ +>1 +CATTCTGCGAAGAAGC +>2 +GGAGAGACGACGTCAATTACT +>3 +AATTTCGAAACTACACCTGGAAGGTAACCA +>4 +ATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT +>5 +TAAGATACTGATAAGGAAACTACCAATA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.tab Sun Jul 02 07:15:35 2017 -0400 @@ -0,0 +1,5 @@ +1 + FBgn0000005_297 1151 CATTCTGCGAAGAAGC +2 + FBgn0000005_297 1167 GGAGAGACGACGTCAATTACT +3 + FBgn0000005_297 1188 AATTTCGAAACTACACCTGGAAGGTAACCA +4 + FBgn0000005_297 1218 ATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT +5 + FBgn0000005_297 1260 TAAGATACTGATAAGGAAACTACCAATA