--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sat Oct 21 09:07:21 2023 +0000
@@ -0,0 +1,95 @@
+<macros>
+    <token name="@TOOL_VERSION@">4.3.6</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">sortmerna</requirement>
+            <requirement type="package" version="1.17">samtools</requirement>
+        </requirements>
+    </xml>
+    <xml name="db_prep">
+        <param name="seed_length" argument="-L" type="integer" min="0" max="100" value="18" label="Seed length" help="Seed length for database indexing"/>
+        <param argument="--max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored"/>
+    </xml>
+    <xml name="reads_macro">
+        <param argument="--reads" type="data" format="fasta,fastq,fastq.gz" label="Querying sequences"/>
+    </xml>
+    <xml name="paired_type_macro">
+        <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not">
+            <option value="">Leave the reads split between aligned and rejected files</option>
+            <option value="--paired_in">Output both reads to aligned file (--paired_in)</option>
+            <option value="--paired_out">Output both reads to rejected file (--paired_out)</option>
+            <option value="--sout">Separate paired and singleton aligned reads (--sout)</option>
+        </param>
+    </xml>
+    <xml name="output_alignments">
+        <param name="print_all_reads" type="boolean" checked="false" truevalue="--print_all_reads" falsevalue="" label="Output null alignment strings for non-aligned reads"/>
+        <conditional name="blast">
+            <param name="blast_output" type="select" label="Output BLAST report?">
+                <option value="True">Yes</option>
+                <option value="False" selected="True">No</option>
+            </param>
+            <when value="True">
+                <param name="blast_format" type="select" label="BLAST-like format?">
+                    <option value="0">pairwise (--blast '0')</option>
+                    <option value="1">tabular BLAST -m 8 format (--blast '1')</option>
+                    <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option>
+                    <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option>
+                    <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option>
+                </param>
+            </when>
+            <when value="False"/>
+        </conditional>
+    </xml>
+    <xml name="otu_picking">
+        <conditional name="otu">
+            <param name="otu_map" type="select" label="Pick OTUs?">
+                <option value="True">Yes</option>
+                <option value="False" selected="true">No</option>
+            </param>
+            <when value="True">
+                <param argument="--id" type="float" value="0.97" label="Percentage id similarity threshold" help="The alignment must still pass the E-value threshold" />
+                <param argument="--coverage" type="float" value="0.97" label="Percentage query coverage threshold" help="The alignment must still pass the E-value threshold" />
+                <param name="de_novo_otu" type="boolean" truevalue="--de_novo_otu" falsevalue="" label="FASTA/FASTQ file for reads matching database below percentage id" help="--de_novo_otu" />
+            </when>
+            <when value="False"/>
+        </conditional>
+    </xml>
+    <token name="@OTU_PICKING@">
+        #if $report.otu.otu_map == 'True'
+            --otu_map
+            --id '$report.otu.id'
+            --coverage '$report.otu.coverage'
+            $report.otu.de_novo_otu
+        #end if
+    </token>
+    <token name="@ALIGNMENTS@">
+        $report.print_all_reads
+        --sam
+        --SQ
+        #if $report.blast.blast_output == 'True'
+            --blast '$report.blast.blast_format'
+        #end if
+    </token>
+    <token name="@PREPROCESSING@">
+        #set $ref = list()
+        #if str( $databases_type.databases_selector ) == 'history'
+            #for $db in $databases_type.database_name
+                $ref.append('%s' % $db )
+            #end for
+        #else
+            #for $db in $databases_type.input_databases
+                $ref.append($db)
+            #end for
+        #end if
+    </token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1093/bioinformatics/bts611</citation>
+            <citation type="doi">10.1093/nar/gks1219</citation>
+            <citation type="doi">10.1093/nar/gks1005</citation>
+            <citation type="doi">10.1093/bioinformatics/btq461</citation>
+            <citation type="doi">10.1038/nbt.2198</citation>
+        </citations>
+    </xml>
+</macros>