--- a/nanopolish_polya.xml	Fri Jul 30 06:29:09 2021 +0000
+++ b/nanopolish_polya.xml	Thu Nov 30 17:59:18 2023 +0000
@@ -1,52 +1,20 @@
-<tool id="nanopolish_polya" name="Nanopolish polyA" version="@VERSION@+galaxy0">
+<tool id="nanopolish_polya" name="Nanopolish polyA" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>- Estimate the length of the poly-A tail on direct RNA reads.</description>
     <macros>
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '$input_merged' reads.fasta && 
-        
-        #if $input_reads_raw.extension == 'fast5':
-            mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 &&
-
-        #else if $input_reads_raw.extension == 'fast5.tar':
-            ln -s '$input_reads_raw' fast5_files.tar &&
-            mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files &&
-
-        #else if $input_reads_raw.extension == 'fast5.tar.bz2':
-            ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
-            mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files &&
-
-        #else:
-            ln -s '$input_reads_raw' fast5_files.tar.gz &&
-            mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files &&
-
-        #end if
-
-        nanopolish index 
-        -d fast5_files/
-        #if $adv.input_seq_summary:
-          -s '$adv.input_seq_summary'
-        #end if 
-        reads.fasta &&
-
-        ln -s '$b' reads.bam &&
-        ln -s '${b.metadata.bam_index}' reads.bam.bai &&
-        #if $reference_source.reference_source_selector == 'history':
-            ln -f -s '$reference_source.ref_file' genome.fa &&
-        #else:
-            ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
-        #end if
+        @PREPROCESS_INPUTS@
         
         nanopolish polya
-        -r reads.fasta
-        -b reads.bam
-        -g genome.fa
-        --threads "\${GALAXY_SLOTS:-4}"        
-        #if $w and str($w).strip():
-          -w "${w}"
-        #end if  
+            -r reads.fasta
+            -b reads.bam
+            -g genome.fa
+            --threads "\${GALAXY_SLOTS:-4}"
+            #if $w and str($w).strip():
+              -w "${w}"
+            #end if  
         > polya_results.tsv
     ]]></command>
     <inputs>
@@ -93,7 +61,16 @@
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" value="enolase_reference.fas" />
             <!-- <param name="w" value="tig00000001:200000-202000" /> -->
-            <output name="polya_results" file="30xpolyA-small-subset-results.tsv" />
+            <output name="polya_results" file="30xpolyA-small-subset-results.tsv" compare="sim_size">
+                <assert_contents>
+                    <has_n_lines n="14"/>
+                    <has_n_columns n="10"/>
+                    <has_line_matching expression="readname\scontig\sposition\sleader_start\sadapter_start\spolya_start\stranscript_start\sread_rate\spolya_length\sqc_tag"/>
+                    <has_text text="453f3f3e-d22f-4d9c-81a6-8576e23390ed"/>
+                    <has_text text="YHR174W"/>
+                    <has_text text="READ_FAILED_LOAD"/>
+                </assert_contents>
+            </output>
         </test>
          <test>
             <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" />
@@ -102,7 +79,16 @@
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" value="enolase_reference.fas" />
             <param name="w" value="YHR174W:600-900" />
-            <output name="polya_results" file="30xpolyA-small-subset-win-results.tsv" />
+            <output name="polya_results" file="30xpolyA-small-subset-win-results.tsv" compare="sim_size">
+                <assert_contents>
+                    <has_n_lines n="12"/>
+                    <has_n_columns n="10"/>
+                    <has_line_matching expression="readname\scontig\sposition\sleader_start\sadapter_start\spolya_start\stranscript_start\sread_rate\spolya_length\sqc_tag"/>
+                    <has_text text="453f3f3e-d22f-4d9c-81a6-8576e23390ed"/>
+                    <has_text text="YHR174W"/>
+                    <has_text text="READ_FAILED_LOAD"/>
+                </assert_contents>
+            </output>
         </test>
          <test>
             <param name="input_merged" ftype="fastq" value="30xpolyA-small-subset.fastq" />
@@ -111,7 +97,16 @@
             <param name="reference_source_selector" value="history" />
             <param name="ref_file" value="enolase_reference.fas" />
             <param name="w" value="YHR174W:600-900" />
-            <output name="polya_results" file="30xpolyA-small-subset-win-results-t3.tsv" />
+            <output name="polya_results" file="30xpolyA-small-subset-win-results-t3.tsv" compare="sim_size">
+                <assert_contents>
+                    <has_n_lines n="12"/>
+                    <has_n_columns n="10"/>
+                    <has_line_matching expression="readname\scontig\sposition\sleader_start\sadapter_start\spolya_start\stranscript_start\sread_rate\spolya_length\sqc_tag"/>
+                    <has_text text="453f3f3e-d22f-4d9c-81a6-8576e23390ed"/>
+                    <has_text text="YHR174W"/>
+                    <has_text text="READ_FAILED_LOAD"/>
+                </assert_contents>
+            </output>
         </test>        
     </tests>    
     <help><![CDATA[