--- a/trycycler_consensus.xml	Mon Dec 13 21:17:36 2021 +0000
+++ b/trycycler_consensus.xml	Sat Dec 18 19:50:44 2021 +0000
@@ -12,9 +12,7 @@
         ln -s '${reconcile_msa}' 'selected_cluster/3_msa.fasta' &&
         ln -s '${partition_reads}' 'selected_cluster/4_reads.fastq' &&
         trycycler consensus --cluster_dir 'selected_cluster'
-            #if $linear
-                --linear
-            #end if
+            $linear
             --min_aligned_len $min_aligned_len
             --min_read_cov $min_read_cov
             --threads \${GALAXY_SLOTS:-2} &&
@@ -24,7 +22,6 @@
         <param name='cluster_all_seqs' type='data' format='fasta' label='Reconciled cluster' help='Reconciled sequences file' />
         <param name='reconcile_msa' type='data' format='fasta' label='Reconcile msa' help='Multiple sequence alignment file' />
         <param name='partition_reads' type='data' format='fastq' label='Partition reads' help='Partitioned reads' />
-        <param name='reads' type='data' format='fastq,fastq.gz' label='Long-read datasets' help='Long reads (FASTQ format) used to generate the assemblies' />
         <param argument='--linear' type='boolean' truevalue='--linear' falsevalue='' label='Input contigs are not circular' help='Use this option if your input contigs are not circular. It will disable the circularisation-correction steps in Trycycler reconcile.' />
         <param argument='--min_aligned_len' type='integer' min='500' max='3500' value='1000' label='Min bases aligned' help='Reads with less than this many bases aligned (default = 1000) will be ignored.' />
         <param argument='--min_read_cov' type='integer' min='0' max='100' value='90' label='Min read length covered by alignments' help='Reads with less than this percentage of their length covered by alignments (default = 90.0) will be ignored.' />
@@ -37,7 +34,6 @@
             <param name='cluster_all_seqs' value='reconciled_cluster_01.fasta' />
             <param name='reconcile_msa' value='aligned_cluster_01.fasta' />
             <param name='partition_reads' value='partition_01.fastq' />
-            <param name='reads' value='reads.fastq.gz' />
             <param name='min_aligned_len' value='1200' />
             <param name='min_read_cov' value='95' />
             <output name='consensus' file='consensus_sequence_01.fasta' />
@@ -46,7 +42,6 @@
             <param name='cluster_all_seqs' value='reconciled_cluster_02.fasta' />
             <param name='reconcile_msa' value='aligned_cluster_02.fasta' />
             <param name='partition_reads' value='partition_01.fastq' />
-            <param name='reads' value='reads.fastq.gz' />
             <param name='min_aligned_len' value='1100' />
             <param name='min_read_cov' value='90' />
             <output name='consensus' file='consensus_sequence_02.fasta' />
@@ -55,7 +50,6 @@
             <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' />
             <param name='reconcile_msa' value='aligned_cluster_03.fasta' />
             <param name='partition_reads' value='partition_01.fastq' />
-            <param name='reads' value='reads.fastq.gz' />
             <param name='min_aligned_len' value='1300' />
             <param name='min_read_cov' value='97' />
             <output name='consensus' file='consensus_sequence_03.fasta' />
@@ -64,7 +58,6 @@
             <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' />
             <param name='reconcile_msa' value='aligned_cluster_03.fasta' />
             <param name='partition_reads' value='partition_01.fastq' />
-            <param name='reads' value='reads.fastq.gz' />
             <param name='min_aligned_len' value='1000' />
             <param name='min_read_cov' value='87' />
             <output name='consensus' file='consensus_sequence_04.fasta' />