Mercurial > repos > artbio > sr_bowtie_dataset_annotation
comparison sr_bowtie_dataset_annotation.xml @ 2:243ed53cbc0d draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 3ca97a7e1b47e4ca94f65ea4639c5aeabb5ed8b2
author | artbio |
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date | Sun, 10 Feb 2019 14:07:12 -0500 |
parents | faf1b3b933f5 |
children | 008de522b3ea |
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1:faf1b3b933f5 | 2:243ed53cbc0d |
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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> |