Mercurial > repos > dfornika > cgview_reformat_blastn_output
changeset 0:90ac002b2098 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cgview commit 9c3f45e4ad61781ac0c3bf61e62d7d94ccb1d4ed-dirty"
| author | dfornika |
|---|---|
| date | Thu, 12 Dec 2019 19:44:51 +0000 |
| parents | |
| children | |
| files | reformat_blastn_output.xml test-data/blastn_output.save.tsv test-data/blastn_output.tsv test-data/blastn_output_reformatted.tsv |
| diffstat | 4 files changed, 61 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reformat_blastn_output.xml Thu Dec 12 19:44:51 2019 +0000 @@ -0,0 +1,36 @@ +<tool id="cgview_reformat_blastn_output" name="reformat blastn output for cgview XML builder" version="1.0+galaxy0"> + <description>Reformat blastn output for cgview_xml_builder</description> + <command detect_errors="exit_code"> + <![CDATA[ + awk -F'\t' 'BEGIN {OFS = FS} $2 = $2 FS "match"' '${input}' | + sed '1iquery_id\tmatch_id\tmatch_description\t%_identity\talignment_length\tmismatches\tgap_openings\tq_start\tq_end\ts_start\ts_end\tevalue\tbit_score' | + sed '1i#PROGRAM=blastn' + > '${output}' + ]]> + </command> + <inputs> + <param name="input" type="data" format="tabular" label="Input" help=""/> + </inputs> + <outputs> + <data name="output" format="tabular"/> + </outputs> + <tests> + </tests> + <help> + </help> + <citations> + <citation type="bibtex"> + @article{ + stothard2004circular, + title={Circular genome visualization and exploration using CGView}, + author={Stothard, Paul and Wishart, David S}, + journal={Bioinformatics}, + volume={21}, + number={4}, + pages={537--539}, + year={2004}, + publisher={Oxford University Press} + } + </citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_output.save.tsv Thu Dec 12 19:44:51 2019 +0000 @@ -0,0 +1,8 @@ +LR595890.1_segment LR595890.1 100.00 9180 0 0 1 9180 23821 33000 0.0 16556 +LR595890.1_segment LR595890.1 75.25 198 49 0 7921 8118 31621 31818 8e-33 136 +LR595890.1_segment LR595890.1 75.25 198 49 0 7801 7998 31741 31938 8e-33 136 +LR595890.1_segment LR595890.1 89.61 77 6 1 1312 1388 56503 56577 6e-22 100 +LR595890.1_segment LR595890.1 74.17 120 31 0 7915 8034 30388 30507 7e-15 77.0 +LR595890.1_segment LR595890.1 74.17 120 31 0 6568 6687 31735 31854 7e-15 77.0 +LR595890.1_segment LR595890.1 84.29 70 7 2 1326 1393 56585 56518 3e-13 71.6 +LR595890.1_segment LR595890.1 79.76 84 8 5 1312 1389 89049 89129 5e-10 60.8
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_output.tsv Thu Dec 12 19:44:51 2019 +0000 @@ -0,0 +1,8 @@ +LR595890.1_segment LR595890.1 100.00 9180 0 0 1 9180 23821 33000 0.0 16556 +LR595890.1_segment LR595890.1 75.25 198 49 0 7921 8118 31621 31818 8e-33 136 +LR595890.1_segment LR595890.1 75.25 198 49 0 7801 7998 31741 31938 8e-33 136 +LR595890.1_segment LR595890.1 89.61 77 6 1 1312 1388 56503 56577 6e-22 100 +LR595890.1_segment LR595890.1 74.17 120 31 0 7915 8034 30388 30507 7e-15 77.0 +LR595890.1_segment LR595890.1 74.17 120 31 0 6568 6687 31735 31854 7e-15 77.0 +LR595890.1_segment LR595890.1 84.29 70 7 2 1326 1393 56585 56518 3e-13 71.6 +LR595890.1_segment LR595890.1 79.76 84 8 5 1312 1389 89049 89129 5e-10 60.8
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blastn_output_reformatted.tsv Thu Dec 12 19:44:51 2019 +0000 @@ -0,0 +1,9 @@ +query_id match_id match_description %_identity alignment_length mismatches gap_openings q_start q_end s_start s_end evalue bit_score +LR595890.1_segment LR595890.1 match 100.00 9180 0 0 1 9180 23821 33000 0.0 16556 +LR595890.1_segment LR595890.1 match 75.25 198 49 0 7921 8118 31621 31818 8e-33 136 +LR595890.1_segment LR595890.1 match 75.25 198 49 0 7801 7998 31741 31938 8e-33 136 +LR595890.1_segment LR595890.1 match 89.61 77 6 1 1312 1388 56503 56577 6e-22 100 +LR595890.1_segment LR595890.1 match 74.17 120 31 0 7915 8034 30388 30507 7e-15 77.0 +LR595890.1_segment LR595890.1 match 74.17 120 31 0 6568 6687 31735 31854 7e-15 77.0 +LR595890.1_segment LR595890.1 match 84.29 70 7 2 1326 1393 56585 56518 3e-13 71.6 +LR595890.1_segment LR595890.1 match 79.76 84 8 5 1312 1389 89049 89129 5e-10 60.8