Mercurial > repos > artbio > sr_bowtie_dataset_annotation
changeset 5:279fdd92a615 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 1d30d780dc66069ae9b52c909f65d713156442b3
| author | artbio |
|---|---|
| date | Sun, 24 Mar 2019 18:23:00 -0400 |
| parents | e11f91575af6 |
| children | 8829656d6999 |
| files | sr_bowtie_dataset_annotation.xml |
| diffstat | 1 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/sr_bowtie_dataset_annotation.xml Wed Mar 20 07:12:53 2019 -0400 +++ b/sr_bowtie_dataset_annotation.xml Sun Mar 24 18:23:00 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.2.0"> +<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.3.0"> <description>by iterative alignments with sRbowtie</description> <requirements> <requirement type="package" version="1.1.2">bowtie</requirement> @@ -13,6 +13,11 @@ #else: #set index_path = $refGenomeSource1.index.fields.path #end if + + #for $i in $AdditionalQueries: + bowtie-build -f $i.ownFile $i.ownFile.name 1>/dev/null && + #end for + #set method_prefix = "-v %s -k 1 --best" % str($mismatches) #if $input[0].is_of_type('fasta'): #set format = "-f" @@ -38,14 +43,13 @@ #else: #set to_align = "matched.fa" #end if - bowtie-build -f $i.ownFile subgenome 1>/dev/null && touch tmp_class_matched.fa tmp_class_unmatched.fa && bowtie -p \${GALAXY_SLOTS:-4} $method_prefix --al tmp_class_matched.fa --un tmp_class_unmatched.fa --suppress 6,7,8 - subgenome $format '$to_align' > tabular_bowtie_output.tab && + $i.ownFile.name $format '$to_align' > tabular_bowtie_output.tab && class_aligned=\$(( \$(wc -l < tmp_class_matched.fa)/2)) && class_unaligned=\$(( \$(wc -l < tmp_class_unmatched.fa)/2)) && echo -e "$sample\t$i.ownFile.name\t\$class_aligned\t\${genome_aligned}" >> $output &&