Mercurial > repos > artbio > sr_bowtie_dataset_annotation
changeset 2:243ed53cbc0d draft
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 |
| files | sr_bowtie_dataset_annotation.xml test-data/sample1_output.tab test-data/sample_output.tab |
| diffstat | 3 files changed, 10 insertions(+), 10 deletions(-) [+] |
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--- a/sr_bowtie_dataset_annotation.xml Sun Feb 10 11:16:59 2019 -0500 +++ b/sr_bowtie_dataset_annotation.xml Sun Feb 10 14:07:12 2019 -0500 @@ -1,4 +1,4 @@ -<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.0.1"> +<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.0.2"> <description>by iterative alignments with sRbowtie</description> <requirements> <requirement type="package" version="1.1.2">bowtie</requirement> @@ -31,9 +31,9 @@ genome_aligned=\$(wc -l < matched.fa) && genome_aligned=\$(( \$genome_aligned/2)) && #if $refGenomeSource1.genomeSource == "history": - echo -e "$refGenomeSource1.ownFile.name Matched\t\${genome_aligned}\n" > $output && + echo -e "$refGenomeSource1.ownFile.name\t\${genome_aligned}\n" > $output && #else: - echo -e "$refGenomeSource1.index.fields.dbkey Matched\t\${genome_aligned}\n" > $output && + echo -e "$refGenomeSource1.index.fields.dbkey\t\${genome_aligned}\n" > $output && #end if #set counter = 0 #for $i in $AdditionalQueries: @@ -57,7 +57,7 @@ class_aligned=\$(( \$(wc -l < temp_class_matched.fa)/2)) && class_unaligned=\$(( \$(wc -l < temp_class_unmatched.fa)/2)) && mv temp_class_unmatched.fa class_unmatched.fa && - echo -e "$i.ownFile.name Matched\t\${class_aligned}\n" >> $output && + echo -e "$i.ownFile.name\t\${class_aligned}\n" >> $output && #end for remaining=\$(( \$(wc -l < class_unmatched.fa)/2)) && echo -e "Unmatched to previous indexes\t\${remaining}\n" >> $output
--- a/test-data/sample1_output.tab Sun Feb 10 11:16:59 2019 -0500 +++ b/test-data/sample1_output.tab Sun Feb 10 14:07:12 2019 -0500 @@ -1,8 +1,8 @@ -2L-tail.fa Matched 2954 +2L-tail.fa 2954 -dme_miR21_hairpin.fa Matched 0 +dme_miR21_hairpin.fa 0 -Ensembl_transposon_set.fa Matched 2689 +Ensembl_transposon_set.fa 2689 Unmatched to previous indexes 265
--- a/test-data/sample_output.tab Sun Feb 10 11:16:59 2019 -0500 +++ b/test-data/sample_output.tab Sun Feb 10 14:07:12 2019 -0500 @@ -1,8 +1,8 @@ -2L-tail.fa Matched 638 +2L-tail.fa 638 -dme_miR21_hairpin.fa Matched 0 +dme_miR21_hairpin.fa 0 -Ensembl_transposon_set.fa Matched 560 +Ensembl_transposon_set.fa 560 Unmatched to previous indexes 78