--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/virAnnot_otu.xml	Wed Aug 21 13:13:10 2024 +0000
@@ -0,0 +1,103 @@
+<tool id="virannot_otu" name="virAnnot OTU" version="1.0.1+galaxy0" profile="21.05">
+    <description>create viral OTUs based on RPS and Blast annotations</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <required_files>
+        <include path="otu.py" />
+        <include path="seek_otu.R" />
+        <include path="rps2tree_html.py" />
+    </required_files>
+    <command detect_errors="aggressive"><![CDATA[
+
+@HEADLESS@
+    #if $blast_files
+        #for $blast_file in $blast_files
+            ln -fs '$blast_file' '$blast_file.element_identifier' &&
+        #end for
+    #end if 
+    #for $rps_file in $rps_files
+        ln -fs '$rps_file' '$rps_file.element_identifier' &&
+    #end for
+    #for $fasta_file in $fasta_files
+        ln -fs '$fasta_file' '$fasta_file.element_identifier' &&
+    #end for
+
+    python '$__tool_directory__/otu.py'
+    #if $blast_files
+        #for $blast_file in $blast_files
+            -b '$blast_file.element_identifier'
+        #end for
+    #end if 
+    #for $rps_file in $rps_files
+        -r '$rps_file.element_identifier'
+    #end for
+    #for $fasta_file in $fasta_files
+        -f '$fasta_file.element_identifier'
+    #end for
+    -p '$percentage'
+    -vp '$viral_portion'
+    -mpl '$min_prot_length'
+    -tp '$__tool_directory__/'
+    -o otu_output
+
+    && zip -r out.zip otu_output
+
+    ]]></command>
+    <inputs>
+        <param type="data" name="blast_files" format="tabular" label="Blast results file with taxonomy" multiple="true" optional="true"
+            help="Give one file per sample. If a file is missing, give none." />
+        <param type="data" name="rps_files" format="tabular" label="RPS results file" multiple="true" />
+        <param type="data" name="fasta_files" format="fasta" label="Contigs file" multiple="true" />
+        <param type="integer" name="percentage" label="Similarity threshold percentage for OTUs cutoff" value="90" min="10" max="100" />
+        <param type="select" name="viral_portion" label="Minimun portion of viral sequences in RPS domain to be included">
+            <option value="0.1">0.1</option>
+            <option value="0.2">0.2</option>
+            <option value="0.3" selected="true">0.3</option>
+            <option value="0.4">0.4</option>
+            <option value="0.5">0.5</option>
+        </param>
+        <param type="select" name="min_prot_length" label="Minimum query protein length">
+            <option value="50">50</option>
+            <option value="80">80</option>
+            <option value="100" selected="true">100</option>
+            <option value="150">150</option>
+            <option value="200">200</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data format="xlsx" name="otu_table" label="${tool.name} on ${on_string}: otu_stats" from_work_dir="otu_output/otu_stats.xlsx" />
+        <data format="zip" name="archive_output" label="${tool.name} on ${on_string}: zip of the complete output" from_work_dir="out.zip" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="blast_files" value="otu_s1_tblastx.tab,otu_s2_tblastx.tab"/>
+            <param name="rps_files" value="otu_s1_rps.tab,otu_s2_rps.tab"/>
+            <param name="fasta_files" value="otu_s1.fa,otu_s2.fa"/>
+            <param name="percentage" value="90"/>
+            <param name="viral_portion" value="0.3"/>
+            <param name="min_prot_length" value="100"/>
+            <!-- check created zip -->
+            <output name="archive_output">
+                <assert_contents>
+                    <has_archive_member path=".*\/index.html" />
+                    <has_archive_member path=".*\/pfam00680_RdRP_1/seq_aligned.final_tree.fa" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+This module takes as input rps file from rps2tsv, blast file from blastxml_to_tabular [optional] and fasta contig file [optional].
+
+If no blast file is given, OTUs will not have an associated annotation i.e the OTUs will be set as unknown.
+Files are processed in alphabetical order. Make sure that the files (blast, rps and contig) for a sample are named in the same way,
+otherwise they will be disassociated.
+
+The standard similarity threshold is 90% [default value] which is a proxy to viral species compared with the ICTV classification.
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>