Mercurial > repos > p.lucas > bt_typer
changeset 1:5656752f1f04 draft
Uploaded wrapper file
| author | p.lucas |
|---|---|
| date | Tue, 26 Mar 2024 09:50:20 +0000 |
| parents | e429156b6075 |
| children | 678581610080 |
| files | Bt_detect_galaxy_wrapper.xml |
| diffstat | 1 files changed, 82 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Bt_detect_galaxy_wrapper.xml Tue Mar 26 09:50:20 2024 +0000 @@ -0,0 +1,82 @@ +<tool id="Bacillus_detection" name="Bacillus Thuringiensis serovars aizaiwai and kurstaki detection" version="1.0"> + <description> + From a 2 blastx output fle (25 columns) and a decision table (default: table_bt.txt) + deduce the Bacillus Thuringiensis serovars aizaiwai and kurstaki. + Provide 1 output txt file with the result. + </description> + <requirements> + <requirement type="package" version="3.7.9">python</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + + <command interpreter="python" detect_errors="exit_code"><![CDATA[ + Bt_detect_galaxy.py + -b "$blastx_output" + -min_id "$min_identity" + -min_cov "$min_coverage" + #if $decision_table.decision_table_select == "default": + -t $__tool_directory__/table_bt.txt + #else: + -t "$decision_table" + #end if + -o "$output" + ]]></command> + <inputs> + <param name="blastx_output" type="data" format="tsv,tabular" label="Blastx output" help="Blastx output file with 25 columns."/> + <param name="min_identity" type="integer" label="Minimum identity" value="90" min="0" max="100" help="Minimum identity to keep the hit" /> + <param name="min_coverage" type="integer" label="Minimum coverage" value="90" min="0" max="100" help="Minimum coverage to keep the hit" /> + <conditional name="decision_table"> + <param name="decision_table_select" type="select" label="Use specific or default decision table?"> + <option value="default" selected="True">Use default decision table.</option> + <option value="specific">Use specific decision table file.</option> + </param> + <when value="default" /> + <when value="specific"> + <param type="data" name="decision_table" format="txt" label="Specific decision table." /> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="output" label="${tool.name} on ${on_string}"/> + </outputs> + <help><![CDATA[ + Tool obtained form github: https://github.com/afelten-Anses/Bt_typing/ + + Bacillus thuringiensis serovars aizaiwai and kurstaki detection from blastx output. + + If you want to use your own detection table, file is configured like this (tabular separator): + + X header lines corresponding to the marker + (name list of reference) + ### (mandatory) + Table with the association between serovar and marker + (column header: "empty header" serovars A serovars B Cluster 1 ...) + (line example: "complete name" 0 -1 1 0...) + + Example with the default file: + + Bt WP_021728236.1|Bt_CwlA WP_000237488.1|Bt_intQ WP_000858032.1|Bt_group_3916 WP_042596929.1|Bt_group_20749 WP_002101540.1|Bt_group_20361 WP_000998670.1|Bt_sdpR + aizaiwai WP_021728520.1|Bta_apr + kurstaki WP_003273526.1|Btk_group_27293 WP_001293418.1|Btk_group_27336 + clusterA WP_000415284.1|clustera_group_10114 + clusterB WP_050062578.1|clusterb_rapF WP_131256056.1|clusterb_group_20667 + clusterC AHZ54004.1|clusterc_lexA + clusterD WP_000791073.1|clusterd_clpP1 + ### + Bt aizaiwai kurstaki clusterA clusterB clusterC clusterD + Bacillus thuringiensis 1 -1 -1 0 0 0 0 + Bacillus thuringiensis 1 1 1 0 0 0 0 + not Bacillus thuringiensis -1 0 0 0 0 0 0 + Bacillus thuringiensis aizaiwai not clustered 1 1 -1 -1 -1 0 0 + Bacillus thuringiensis aizaiwai not clustered 1 1 -1 1 1 0 0 + Bacillus thuringiensis kurstaki not clustered 1 -1 1 0 0 -1 -1 + Bacillus thuringiensis kurstaki not clustered 1 -1 1 0 0 1 1 + Bacillus thuringiensis aizaiwai cluster A 1 1 -1 1 -1 0 0 + Bacillus thuringiensis aizaiwai cluster B 1 1 -1 -1 1 0 0 + Bacillus thuringiensis kurstaki cluster C 1 -1 1 0 0 1 -1 + Bacillus thuringiensis kurstaki cluster D 1 -1 1 0 0 -1 1 + + ]]></help> +