Mercurial > repos > artbio > sr_bowtie_dataset_annotation
comparison sr_bowtie_dataset_annotation.xml @ 5:279fdd92a615 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 1d30d780dc66069ae9b52c909f65d713156442b3
| author | artbio |
|---|---|
| date | Sun, 24 Mar 2019 18:23:00 -0400 |
| parents | e11f91575af6 |
| children | 8829656d6999 |
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| 4:e11f91575af6 | 5:279fdd92a615 |
|---|---|
| 1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.2.0"> | 1 <tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.3.0"> |
| 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 <requirement type="package" version="1.6.0">r-optparse</requirement> | 5 <requirement type="package" version="1.6.0">r-optparse</requirement> |
| 6 <requirement type="package" version="3.1.0">r-ggplot2</requirement> | 6 <requirement type="package" version="3.1.0">r-ggplot2</requirement> |
| 11 bowtie-build -f $refGenomeSource1.ownFile genome 1>/dev/null && | 11 bowtie-build -f $refGenomeSource1.ownFile genome 1>/dev/null && |
| 12 #set index_path = 'genome' | 12 #set index_path = 'genome' |
| 13 #else: | 13 #else: |
| 14 #set index_path = $refGenomeSource1.index.fields.path | 14 #set index_path = $refGenomeSource1.index.fields.path |
| 15 #end if | 15 #end if |
| 16 | |
| 17 #for $i in $AdditionalQueries: | |
| 18 bowtie-build -f $i.ownFile $i.ownFile.name 1>/dev/null && | |
| 19 #end for | |
| 20 | |
| 16 #set method_prefix = "-v %s -k 1 --best" % str($mismatches) | 21 #set method_prefix = "-v %s -k 1 --best" % str($mismatches) |
| 17 #if $input[0].is_of_type('fasta'): | 22 #if $input[0].is_of_type('fasta'): |
| 18 #set format = "-f" | 23 #set format = "-f" |
| 19 #elif $input[0].is_of_type('fastq'): | 24 #elif $input[0].is_of_type('fastq'): |
| 20 #set format = "-q" | 25 #set format = "-q" |
| 36 #if $counter != 1: | 41 #if $counter != 1: |
| 37 #set to_align = "class_unmatched.fa" | 42 #set to_align = "class_unmatched.fa" |
| 38 #else: | 43 #else: |
| 39 #set to_align = "matched.fa" | 44 #set to_align = "matched.fa" |
| 40 #end if | 45 #end if |
| 41 bowtie-build -f $i.ownFile subgenome 1>/dev/null && | |
| 42 touch tmp_class_matched.fa tmp_class_unmatched.fa && | 46 touch tmp_class_matched.fa tmp_class_unmatched.fa && |
| 43 bowtie -p \${GALAXY_SLOTS:-4} | 47 bowtie -p \${GALAXY_SLOTS:-4} |
| 44 $method_prefix | 48 $method_prefix |
| 45 --al tmp_class_matched.fa | 49 --al tmp_class_matched.fa |
| 46 --un tmp_class_unmatched.fa | 50 --un tmp_class_unmatched.fa |
| 47 --suppress 6,7,8 | 51 --suppress 6,7,8 |
| 48 subgenome $format '$to_align' > tabular_bowtie_output.tab && | 52 $i.ownFile.name $format '$to_align' > tabular_bowtie_output.tab && |
| 49 class_aligned=\$(( \$(wc -l < tmp_class_matched.fa)/2)) && | 53 class_aligned=\$(( \$(wc -l < tmp_class_matched.fa)/2)) && |
| 50 class_unaligned=\$(( \$(wc -l < tmp_class_unmatched.fa)/2)) && | 54 class_unaligned=\$(( \$(wc -l < tmp_class_unmatched.fa)/2)) && |
| 51 echo -e "$sample\t$i.ownFile.name\t\$class_aligned\t\${genome_aligned}" >> $output && | 55 echo -e "$sample\t$i.ownFile.name\t\$class_aligned\t\${genome_aligned}" >> $output && |
| 52 mv tmp_class_unmatched.fa class_unmatched.fa && | 56 mv tmp_class_unmatched.fa class_unmatched.fa && |
| 53 rm tmp_class_matched.fa && | 57 rm tmp_class_matched.fa && |