Mercurial > repos > artbio > sr_bowtie_dataset_annotation

comparison sr_bowtie_dataset_annotation.xml @ 2:243ed53cbc0d draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 3ca97a7e1b47e4ca94f65ea4639c5aeabb5ed8b2
author artbio
date Sun, 10 Feb 2019 14:07:12 -0500
parents faf1b3b933f5
children 008de522b3ea
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1:faf1b3b933f5 2:243ed53cbc0d
1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.0.1"> 1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.0.2">
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[
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 #if $refGenomeSource1.genomeSource == "history": 33 #if $refGenomeSource1.genomeSource == "history":
34 echo -e "$refGenomeSource1.ownFile.name Matched\t\${genome_aligned}\n" > $output && 34 echo -e "$refGenomeSource1.ownFile.name\t\${genome_aligned}\n" > $output &&
35 #else: 35 #else:
36 echo -e "$refGenomeSource1.index.fields.dbkey Matched\t\${genome_aligned}\n" > $output && 36 echo -e "$refGenomeSource1.index.fields.dbkey\t\${genome_aligned}\n" > $output &&
37 #end if 37 #end if
38 #set counter = 0 38 #set counter = 0
39 #for $i in $AdditionalQueries: 39 #for $i in $AdditionalQueries:
40 rm -f genome.fa && 40 rm -f genome.fa &&
41 #set $counter += 1 41 #set $counter += 1
55 --suppress 6,7,8 55 --suppress 6,7,8
56 $index_path $format '$input' > tabular_bowtie_output.tab && 56 $index_path $format '$input' > tabular_bowtie_output.tab &&
57 class_aligned=\$(( \$(wc -l < temp_class_matched.fa)/2)) && 57 class_aligned=\$(( \$(wc -l < temp_class_matched.fa)/2)) &&
58 class_unaligned=\$(( \$(wc -l < temp_class_unmatched.fa)/2)) && 58 class_unaligned=\$(( \$(wc -l < temp_class_unmatched.fa)/2)) &&
59 mv temp_class_unmatched.fa class_unmatched.fa && 59 mv temp_class_unmatched.fa class_unmatched.fa &&
60 echo -e "$i.ownFile.name Matched\t\${class_aligned}\n" >> $output && 60 echo -e "$i.ownFile.name\t\${class_aligned}\n" >> $output &&
61 #end for 61 #end for
62 remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) && 62 remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) &&
63 echo -e "Unmatched to previous indexes\t\${remaining}\n" >> $output 63 echo -e "Unmatched to previous indexes\t\${remaining}\n" >> $output
64 ]]></command> 64 ]]></command>
65 <inputs> 65 <inputs>