--- a/trycycler_reconcile_msa.xml	Mon Dec 13 21:16:05 2021 +0000
+++ b/trycycler_reconcile_msa.xml	Wed Mar 29 20:24:48 2023 +0000
@@ -8,7 +8,7 @@
     <version_command>trycycler --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
         #import re
-        #set $name = re.sub('[^\w\-\.]', '_', str($input_cluster.element_identifier))
+        #set $name = re.sub('[^\w\-\.]', '_', str($input_cluster.element_identifier)+".fasta")
         #set $folder = $name.strip(".fasta")
         #set $fullpath = "/".join(["selected_cluster",$folder])
         mkdir -p "${fullpath}/1_contigs" &&
@@ -26,7 +26,7 @@
             --max_trim_seq $circularisation.max_trim_seq
             --max_trim_seq_percent $circularisation.max_trim_seq_percent
             --min_identity $final_check.min_identity
-            --max_indel_size $final_check.max_indel_size
+            --min_1kbp_identity $final_check.min_1kbp_identity
             --threads \${GALAXY_SLOTS:-2} &&
         trycycler msa --cluster_dir "$fullpath"
             --kmer $msa.kmer
@@ -52,7 +52,7 @@
         </section>
         <section name="final_check" title="Reconcile final check" expanded="true">
             <param argument="--min_identity" type="integer" min="70" max="100" value="98" label="Min global alignment percentage identity" help="If any of the sequences have a pairwise global alignment percent identity of less than this (default = 98), then the contigs will fail the final check." />
-            <param argument="--max_indel_size" type="integer" min="0" max="10000" value="1000" label="Max alignment indel size" help="If any of the sequences have a pairwise alignment indel size of more than this (default = 1000), then the contigs will fail the final check." />
+            <param argument="--min_1kbp_identity" type="integer" min="0" value="25" label="Minimum allowed pairwise 1kbp window identity" help="If any of the sequences have lower pairwise window identity, it is discarted." />
         </section>
         <section name="msa" title="Multiple sequence alignment (MSA) options" expanded="true">
             <param argument="--kmer" type="integer" min="20" max="45" value="32" label="k-mer size" help="The k-mer size used for sequence partitioning (default = 32)" />
@@ -83,7 +83,7 @@
                 <param name="max_trim_seq" value="47000" />
             </section>
             <section name="final_check">
-                <param name="max_indel_size" value="230" />
+                <param name="min_1kbp_identity" value="30" />
             </section>
             <section name="msa">
                 <param name="kmer" value="30" />
@@ -122,7 +122,7 @@
             </section>
             <section name="final_check">
                 <param name="min_identity" value="95" />
-                <param name="max_indel_size" value="230" />
+                <param name="min_1kbp_identity" value="25" />
             </section>
             <section name="msa">
                 <param name="kmer" value="33" />
@@ -150,7 +150,27 @@
             <output name='reconciled_cluster' file='reconciled_cluster_05.fasta' />
             <output name='aligned_cluster' file='aligned_cluster_05.fasta' />
         </test>
-
+        <test>
+            <!-- Use similar collection elmement file id as input (wihout extension)-->
+            <param name='input_cluster' value='cluster_01' />
+            <param name="reads" value="reads.fastq.gz" />
+            <section name="initial_check">
+                <param name="max_mash_dist" value="0.3" />
+            </section>
+            <section name="circularisation">
+                <param name="max_add_seq_percentage" value="8" />
+                <param name="max_trim_seq" value="45300" />
+            </section>
+            <section name="final_check">
+                <param name="min_identity" value="97" />
+            </section>
+            <section name="msa">
+                <param name="step" value="1100" />
+                <param name="lookahead" value="980" />
+            </section>
+            <output name='reconciled_cluster' file='reconciled_cluster_05.fasta' />
+            <output name='aligned_cluster' file='aligned_cluster_05.fasta' />
+        </test>
     </tests>
     <help><![CDATA[