# HG changeset patch
# User p.lucas
# Date 1711446620 0
# Node ID 5656752f1f0481fa4c0f4adf25f3a600b53d0f4f
# Parent  e429156b6075919484b2f9bc1302fa1602f7e43f
Uploaded wrapper file

diff -r e429156b6075 -r 5656752f1f04 Bt_detect_galaxy_wrapper.xml
--- /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>
+