Mercurial > repos > artbio > sr_bowtie_dataset_annotation
comparison sr_bowtie_dataset_annotation.xml @ 1:faf1b3b933f5 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit ea052763fe969f830a1ed17e5ffac07146e8d4e9
author | artbio |
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date | Sun, 10 Feb 2019 11:16:59 -0500 |
parents | e7e7785e41d0 |
children | 243ed53cbc0d |
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0:e7e7785e41d0 | 1:faf1b3b933f5 |
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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" |