handle review comments and fix failing tests

Author: Smeds

tools/telogator2/macros.xml

@@ -31,7 +31,7 @@
     </xml>
     <xml name="citations">
         <citations>
-            <citation type="doi">10.1186/s12859-024-05814-5</citation>
+            <citation type="doi">10.1186/s12859-024-05807-5</citation>
         </citations>
     </xml>
 </macros>

tools/telogator2/telogator2.xml

@@ -86,9 +86,7 @@
         --filt-nontel '${advanced.filtering.filt_nontel}'
         --filt-sub '${advanced.filtering.filt_sub}'
         --collapse-hom '${advanced.filtering.collapse_hom}'
-        #if $advanced.filtering.fast_aln
-            --fast-aln
-        #end if
+        '${advanced.filtering.fast_aln}'
 
         ## Hierarchical clustering parameters
         -t0 '${advanced.clustering.t0}'
@@ -112,7 +110,7 @@
         && mv output_dir/violin_atl.png '${output_violin_plot}'
     ]]></command>
     <inputs>
-        <param name="input_reads" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz,fastq,fastq.gz,bam,cram" multiple="true" label="Input reads" help="Long-read sequencing data in FASTA, FASTQ, BAM, or CRAM format (gzipped supported). Multiple files can be selected."/>
+        <param name="input_reads" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz,bam,cram" multiple="true" label="Input reads" help="Long-read sequencing data in FASTA, FASTQ, BAM, or CRAM format (gzipped supported). Multiple files can be selected."/>
 
         <param name="read_type" type="select" label="Read type" help="Sequencing platform type">
             <option value="ont">Oxford Nanopore (ONT)</option>
@@ -129,8 +127,8 @@
                 <option value="median">Median</option>
                 <option value="max">Maximum</option>
             </param>
-            <param name="downsample" argument="-d" type="integer" optional="true" label="Downsample telomere reads" help="Downsample to N telomere reads (optional)"/>
-            <param name="random_seed" argument="--rng" type="integer" optional="true" label="Random seed" help="Random seed value for reproducibility (optional)"/>
+            <param name="downsample" argument="-d" type="integer" optional="true" value="" label="Downsample telomere reads" help="Downsample to N telomere reads (optional)"/>
+            <param name="random_seed" argument="--rng" type="integer" optional="true" value="" label="Random seed" help="Random seed value for reproducibility (optional)"/>
         </section>
 
         <section name="reference_opts" title="Reference Options" expanded="false">
@@ -159,7 +157,7 @@
                 <param argument="--filt-nontel" type="integer" value="100" min="0" label="Maximum terminating non-telomere" help="Maximum terminating non-telomere length in bp"/>
                 <param argument="--filt-sub" type="integer" value="1000" min="0" label="Minimum terminating subtelomere" help="Minimum terminating subtelomere length in bp"/>
                 <param argument="--collapse-hom" type="integer" value="1000" min="0" label="Collapse homologous alleles" help="Merge alleles within this distance in bp"/>
-                <param argument="--fast-aln" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use fast alignment" help="Use faster but less accurate pairwise alignment"/>
+                <param argument="--fast-aln" type="boolean" truevalue="--fast-aln" falsevalue="" checked="false" label="Use fast alignment" help="Use faster but less accurate pairwise alignment"/>
             </section>
 
             <section name="clustering" title="Hierarchical Clustering (TREECUT) Parameters" expanded="false">
@@ -201,7 +199,7 @@
                     <has_text text="allele_id"/>
                     <has_text text="TL_p75"/>
                     <has_n_columns n="11"/>
-                    <has_n_lines n="2" delta="10"/>
+                    <has_n_lines n="13" delta="2"/>
                     <has_line_matching expression="chr\d+[pq]\t\d+.*"/>
                 </assert_contents>
             </output>
@@ -258,7 +256,7 @@
                     <has_text text="allele_id"/>
                     <has_text text="TL_p75"/>
                     <has_n_columns n="11"/>
-                    <has_n_lines n="2" delta="10"/>
+                    <has_n_lines n="13" delta="2"/>
                 </assert_contents>
             </output>
             <output name="output_alleles_plot">
@@ -286,7 +284,7 @@
                     <has_text text="allele_id"/>
                     <has_text text="TL_p75"/>
                     <has_n_columns n="11"/>
-                    <has_n_lines n="2" delta="10"/>
+                    <has_n_lines n="13" delta="2"/>
                 </assert_contents>
             </output>
             <output name="output_alleles_plot">
@@ -351,9 +349,6 @@ The tool performs the following analyses:
 - Runtime improves with additional CPU cores (increase processes parameter)
 - Alleles with suffix 'i' are interstitial telomeric regions and may need to be excluded from downstream analysis
 
-**Reference**
-
-Stephens, Z., & Kocher, J. P. (2024). Characterization of telomere variant repeats using long reads enables allele-specific telomere length estimation. BMC Bioinformatics, 25(1), 194.
     ]]></help>
     <expand macro="citations"/>
 </tool>