--- a/ivar_removereads.xml	Fri Jun 11 15:35:33 2021 +0000
+++ b/ivar_removereads.xml	Thu Aug 05 12:39:31 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy0">
+<tool id="ivar_removereads" name="ivar removereads" version="@VERSION@+galaxy1">
     <description>Remove reads from trimmed BAM file</description>
     <macros>
         <import>macros.xml</import>
@@ -10,11 +10,15 @@
     <command detect_errors="exit_code"><![CDATA[
         cp '$input_bed' binding_sites.bed &&
         python '$__tool_directory__/sanitize_bed.py' binding_sites.bed &&
-
+        #if $amplicons.computed == "yes"
+            python '$__tool_directory__/write_amplicon_info_file.py' binding_sites.bed amplicon_info.tsv &&
+        #else
+            ln -s '$amplicon_info' amplicon_info.tsv &&
+        #end if
         ivar getmasked
-        -i '$variants_tsv' -b binding_sites.bed -f '$amplicon_info' -p masked_primers &&
+        -i '$variants_tsv' -b binding_sites.bed -f amplicon_info.tsv -p masked_primers &&
 
-        python '$__tool_directory__/completemask.py' masked_primers.txt '$amplicon_info' &&
+        python '$__tool_directory__/completemask.py' masked_primers.txt amplicon_info.tsv &&
         ln -s '$input_bam' sorted.bam &&
         ln -s '${input_bam.metadata.bam_index}' sorted.bam.bai &&
 
@@ -33,9 +37,18 @@
         help="This dataset will be scanned for variants that affect primer binding sites and needs to be in tabular format with affected chromosome names in the first, and positions in the second column. If there is a header line, the name of the second column should be POS." />
         <param name="input_bed" argument="-b" type="data" format="bed" label="Primer binding sites information"
         help="The same six-column BED dataset that served as input to ivar trim"/>
-        <param name="amplicon_info" type="data" format="tabular"
-        label="Primer to amplicon assignment info"
-        help="This input should consist of one line per amplicon with the tab-separated names of all primers used to generate that amplicon."/>
+        <conditional name="amplicons">
+            <param name="computed" type="select" label="Compute amplicon info from BED file" help="Compute the amplicon info file from the primer BED file">
+                <option value="yes" selected="true">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes" />
+            <when value="no">
+                <param name="amplicon_info" type="data" format="tabular"
+                label="Primer to amplicon assignment info"
+                help="This input should consist of one line per amplicon with the tab-separated names of all primers used to generate that amplicon."/>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
         <data name="output_bam" format="bam" label="${tool.name} on ${on_string}" from_work_dir="removed_reads.bam"/>
@@ -45,7 +58,19 @@
             <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
             <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/>
             <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/>
-            <param name="amplicon_info" value="zika/db/pair_information.tsv"/>
+            <conditional name="amplicons">
+                <param name="computed" value="no" />
+                <param name="amplicon_info" value="zika/db/pair_information.tsv"/>
+            </conditional>
+            <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" />
+        </test>
+        <test>
+            <param name="input_bam" value="zika/Z52_a.trimmed.sorted.bam"/>
+            <param name="variants_tsv" value="zika/primers_Z52_consensus.tsv"/>
+            <param name="input_bed" value="zika/db/zika_primers_consensus.bed"/>
+            <conditional name="amplicons">
+                <param name="computed" value="yes" />
+            </conditional>
             <output name="output_bam" file="zika/Z52_a.masked.bam" compare="sim_size" delta="100000" />
         </test>
     </tests>