Mercurial > repos > artbio > sr_bowtie_dataset_annotation

comparison sr_bowtie_dataset_annotation.xml @ 1:faf1b3b933f5 draft

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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
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0:e7e7785e41d0 1:faf1b3b933f5
1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.0.0"> 1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.0.1">
2 <description>by iterative alignments with sRbowtie</description> 2 <description>by iterative alignments with sRbowtie</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.1.2">bowtie</requirement> 4 <requirement type="package" version="1.1.2">bowtie</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
28 --un unmatched.fa 28 --un unmatched.fa
29 --suppress 6,7,8 29 --suppress 6,7,8
30 $index_path $format '$input' > tabular_bowtie_output.tab && 30 $index_path $format '$input' > tabular_bowtie_output.tab &&
31 genome_aligned=\$(wc -l < matched.fa) && 31 genome_aligned=\$(wc -l < matched.fa) &&
32 genome_aligned=\$(( \$genome_aligned/2)) && 32 genome_aligned=\$(( \$genome_aligned/2)) &&
33 echo -e "$refGenomeSource1.ownFile.name Matched\t\${genome_aligned}\n" > $output && 33 #if $refGenomeSource1.genomeSource == "history":
34 echo -e "$refGenomeSource1.ownFile.name Matched\t\${genome_aligned}\n" > $output &&
35 #else:
36 echo -e "$refGenomeSource1.index.fields.dbkey Matched\t\${genome_aligned}\n" > $output &&
37 #end if
34 #set counter = 0 38 #set counter = 0
35 #for $i in $AdditionalQueries: 39 #for $i in $AdditionalQueries:
36 rm genome.fa && 40 rm -f genome.fa &&
37 #set $counter += 1 41 #set $counter += 1
38 #if $counter != 1: 42 #if $counter != 1:
39 #set input = "class_unmatched.fa" 43 #set input = "class_unmatched.fa"
40 #else: 44 #else:
41 #set input = "matched.fa" 45 #set input = "matched.fa"