--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/virAnnot_blast2tsv.xml	Mon Mar 04 19:55:52 2024 +0000
@@ -0,0 +1,94 @@
+<tool id="virannot_blast2tsv" name="virAnnot Blast2tsv" version="1.0.0+galaxy0" profile="21.05">
+    <description>convert XML blast results to tabular file with taxonomic informations</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <required_files>
+        <include path="blast2tsv.py" />
+    </required_files>
+    <command detect_errors="aggressive"><![CDATA[
+    python '$__tool_directory__/blast2tsv.py' 
+        -x '$blast_xml' 
+        -c '$contigs' 
+        -a '$blast_type' 
+        -me '$max_evalue'
+        #if $read_nb
+            -rn '$read_nb'
+        #end if
+    ]]></command>
+    <inputs>
+        <param type="data" name="blast_xml" format="blastxml" label="Blast results file" />
+        <param type="data" name="contigs" format="fasta" label="Contigs" />
+        <param type="select" name="blast_type" label="Type of blast">
+            <option value="BLASTX">BLASTX</option>
+            <option value="BLASTP">BLASTP</option>
+            <option value="TBLASTX" selected="true">TBLASTX</option>
+            <option value="BLASTN">BLASTN</option>
+            <option value="DIAMOND">DIAMOND</option>
+        </param>
+        <param type="select" name="max_evalue" label="Maximum evalue">
+            <option value="0">0</option>
+            <option value="0.1">0.1</option>
+            <option value="0.01">0.01</option>
+            <option value="0.001" selected="true">0.001</option>
+            <option value="0.0001">0.0001</option>
+        </param>
+        <param type="data" name="read_nb" format="tabular" label="Read number file" optional="true" />
+    </inputs>
+    <outputs>
+        <data name="out_annotation" format="tabular" from_work_dir="blast2tsv/blast2tsv_output.tab" label="${tool.name} on ${on_string} : annotation" />
+        <data name="out_reads" format="tabular" from_work_dir="blast2tsv/blast2tsv_reads.txt" label="${tool.name} on ${on_string} : output reads" />
+        <data name="out_contigs" format="tabular" from_work_dir="blast2tsv/blast2tsv_contigs.txt" label="${tool.name} on ${on_string} : output contigs" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="blast_xml" value="blast2tsv_input.xml"/>
+            <param name="contigs" value="blast2tsv_contigs.fa"/>
+            <param name="blast_type" value="TBLASTX"/>
+            <param name="max_evalue" value="0.001"/>
+            <output name="out_annotation" file="blast2tsv_output.tab">
+                <assert_contents>
+                    <has_n_columns n="16" />
+                    <has_n_lines n="6" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="blast_xml" value="blast2tsv_input.xml"/>
+            <param name="contigs" value="blast2tsv_contigs.fa"/>
+            <param name="blast_type" value="TBLASTX"/>
+            <param name="max_evalue" value="0.001"/>
+            <output name="out_annotation" file="blast2tsv_output.tab">
+                <assert_contents>
+                    <has_text text="NC_011554" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="blast_xml" value="blast2tsv_input.xml"/>
+            <param name="contigs" value="blast2tsv_contigs.fa"/>
+            <param name="blast_type" value="TBLASTX"/>
+            <param name="max_evalue" value="0.001"/>
+            <param name="read_nb" value="blast2tsv_read_nb.tab"/>
+            <output name="out_annotation" file="blast2tsv_output_with_rn.tab">
+                <assert_contents>
+                    <has_text text="402" />
+                </assert_contents>
+            </output>
+            <output name="out_annotation" file="blast2tsv_reads_with_rn.txt">
+                <assert_contents>
+                    <has_text text="8" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        
+This module takes as input blast file from blast annotation and fasta contig file.
+Set the right blast type or else the query overlap and hit overlap values will be wrong.
+For TBLASTX type, the standard maximum evalue is 0.001.
+
+    ]]></help>
+    <expand macro="citations"/><!--rajouter ete3-->
+</tool>