--- a/varvamp.xml	Sat Jun 15 15:43:28 2024 +0000
+++ b/varvamp.xml	Thu Oct 24 18:10:50 2024 +0000
@@ -8,14 +8,17 @@
     </xrefs>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">varvamp</requirement>
-        <requirement type="package" version="2.0.1">primer3-py</requirement>
+        <requirement type="package" version="2.0.3">primer3-py</requirement>
         <requirement type="package" version="0.7.17">seqfold</requirement>
+        <requirement type="package" version="3.12">python</requirement>
+        <requirement type="package" version="9.5">coreutils</requirement>
     </requirements>
     <version_command>varvamp --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
 VARVAMP_CONFIG=custom_config varvamp
 
 $mode.m_select
+--name '$mode.name'
 #if $mode.main_params.specify_how in ("set_threshold", "set_both"):
   --threshold $mode.main_params.threshold
 #end if
@@ -47,13 +50,18 @@
 '$alignment'
 results/
 
+#if $mode.scheme_outputs and 'primer_binding_sites' in $mode.scheme_outputs:
+  ## the leading header line written by this version of the tool
+  ## is less than helpful in that in can cause parsing issues with downstream tools like ivar trim
+  && tail -n +2 results/primers.bed > results/primers_headerless.bed
+#end if
 #if $mode.m_select == 'qpcr' and $mode.scheme_outputs and 'primer_seqs' in $mode.scheme_outputs:
   ## make the primer sequences fasta discoverable under the same name that is used in "single" mode
   && mv results/oligos.fasta results/primers.fasta
 #end if
 #if $mode.m_select == 'tiled' and $mode.scheme_outputs and 'primer_dimers' in $mode.scheme_outputs:
   ## ensure the unsolvable_primer_dimers.tsv file, which varVAMP creates only conditionally, exists in all cases, in which we try to discover it as an output
-  && cp -n dimers_fallback.tsv results/unsolvable_primer_dimers.tsv
+  && cp --update=none dimers_fallback.tsv results/unsolvable_primer_dimers.tsv
 #end if
     ]]></command>
     <configfiles>
@@ -118,6 +126,7 @@
                 <option value="qpcr">qPCR primers (qpcr)</option>
             </param>
             <when value="single">
+                <param argument="--name" type="text" value="AMPLICON" label="Name your amplicon" help="This name will be used in various outputs of the tool." />
                 <expand macro="main_parameters" />
                 <expand macro="amplicon_length_restrictions" />
                 <expand macro="blast_options" />
@@ -142,6 +151,7 @@
                 </expand>
             </when>
             <when value="tiled">
+                <param argument="--name" type="text" value="TILED_SCHEME" label="Name your primer scheme" help="This name will be used in various outputs of the tool." />
                 <expand macro="main_parameters" />
                 <expand macro="amplicon_length_restrictions" />
                 <param argument="--overlap" type="integer" min="1" value="100" label="Minimal required overlap between tiled amplicons" help="default: 100" />
@@ -158,6 +168,7 @@
                 </expand>
             </when>
             <when value="qpcr">
+                <param argument="--name" type="text" value="QPCR_SCHEME" label="Name your qPCR scheme" help="This name will be used in various outputs of the tool." />
                 <expand macro="main_parameters">
                     <param argument="--pn-ambig" type="integer" min="0" value="1" label="Maximum number of ambiguous nucleotides per qPCR probe to be tolerated" help="To enforce specificity of detection, varVAMP will refuse to work if you set this value higher than for the amplicon primers above, and you may actually want to set it slightly lower than that value." />
                 </expand>
@@ -210,10 +221,10 @@
         </data>
         <collection name="primer_seqs_collection" type="list" label="${tool.name} on ${on_string}: per-pool primer sequences">
             <filter>mode['m_select'] == 'tiled' and mode['scheme_outputs'] and 'primer_seqs' in mode['scheme_outputs']</filter>
-            <data name="pool1_sequences" format="fasta" from_work_dir="results/primers_pool_0.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 1 primers" />
-            <data name="pool2_sequences" format="fasta" from_work_dir="results/primers_pool_1.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 2 primers" />
+            <data name="pool1_sequences" format="fasta" from_work_dir="results/primers_pool_1.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 1 primers" />
+            <data name="pool2_sequences" format="fasta" from_work_dir="results/primers_pool_2.fasta" label="${tool.name} on ${on_string}: Sequences of designed pool 2 primers" />
         </collection>
-        <data name="primers_bed" format="bed" from_work_dir="results/primers.bed" label="${tool.name} on ${on_string}: Primer binding sites">
+        <data name="primers_bed" format="bed" from_work_dir="results/primers_headerless.bed" label="${tool.name} on ${on_string}: Primer binding sites">
             <filter>mode['scheme_outputs'] and 'primer_binding_sites' in mode['scheme_outputs']</filter>
         </data>
         <data name="amplicons_bed" format="bed" from_work_dir="results/amplicons.bed" label="${tool.name} on ${on_string}: Amplicon locations">
@@ -344,13 +355,13 @@
                 <element name="pool1_sequences" ftype="fasta">
                     <assert_contents>
                         <has_n_lines n="4"/>
-                        <has_line line=">AMPLICON_0_LEFT"/>
+                        <has_line line=">TILED_SCHEME_0_LEFT"/>
                     </assert_contents>
                 </element>
                 <element name="pool2_sequences" ftype="fasta">
                     <assert_contents>
                         <has_n_lines n="4"/>
-                        <has_line line=">AMPLICON_1_LEFT"/>
+                        <has_line line=">TILED_SCHEME_1_LEFT"/>
                     </assert_contents>
                 </element>
             </output_collection>