Mercurial > repos > artbio > sr_bowtie_dataset_annotation
changeset 1:faf1b3b933f5 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit ea052763fe969f830a1ed17e5ffac07146e8d4e9
| author | artbio |
|---|---|
| date | Sun, 10 Feb 2019 11:16:59 -0500 |
| parents | e7e7785e41d0 |
| children | 243ed53cbc0d |
| files | sr_bowtie_dataset_annotation.xml |
| diffstat | 1 files changed, 7 insertions(+), 3 deletions(-) [+] |
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--- a/sr_bowtie_dataset_annotation.xml Mon Sep 11 18:27:40 2017 -0400 +++ b/sr_bowtie_dataset_annotation.xml Sun Feb 10 11:16:59 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.0.0"> +<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.0.1"> <description>by iterative alignments with sRbowtie</description> <requirements> <requirement type="package" version="1.1.2">bowtie</requirement> @@ -30,10 +30,14 @@ $index_path $format '$input' > tabular_bowtie_output.tab && genome_aligned=\$(wc -l < matched.fa) && genome_aligned=\$(( \$genome_aligned/2)) && - echo -e "$refGenomeSource1.ownFile.name Matched\t\${genome_aligned}\n" > $output && + #if $refGenomeSource1.genomeSource == "history": + echo -e "$refGenomeSource1.ownFile.name Matched\t\${genome_aligned}\n" > $output && + #else: + echo -e "$refGenomeSource1.index.fields.dbkey Matched\t\${genome_aligned}\n" > $output && + #end if #set counter = 0 #for $i in $AdditionalQueries: - rm genome.fa && + rm -f genome.fa && #set $counter += 1 #if $counter != 1: #set input = "class_unmatched.fa"