--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hifiadapterfilt.xml	Mon Jul 11 03:09:58 2022 +0000
@@ -0,0 +1,98 @@
+<tool id="hifiadapterfilt" name="HiFi Adapter Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" >
+    <description>Remove CCS reads with remnant PacBio adapter sequences</description>
+    <xrefs>
+        <xref type='bio.tools'>hifiadapterfilt</xref>
+    </xrefs>
+    <macros>
+	  <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command><![CDATA[
+
+	    @CLEAN_EXT@
+
+	    #if $input_file.is_of_type("fastq.gz"):
+	    	#set $inputfile = $clean_ext($input_file.element_identifier) + '.fastq.gz'
+		#set prefix = $clean_ext($input_file.element_identifier)
+	    #elif $input_file.is_of_type("fastq"):
+	        #set $inputfile = $clean_ext($input_file.element_identifier) + '.fastq'
+	        #set prefix = $clean_ext($input_file.element_identifier)
+	    #elif $input_file.is_of_type("bam"):
+	    	#set $inputfile = $clean_ext($input_file.element_identifier) + '.bam'
+                #set prefix = $clean_ext($input_file.element_identifier)
+	    #end if
+	    ln -s '${input_file}' '${inputfile}' &&
+
+	    bash pbadapterfilt.sh
+            -p '$prefix'
+	    -l '$match_length'
+	    -m '$match_percentage'            
+	    -t\${GALAXY_SLOTS:-4}
+	    -o . 
+	    && cp '$prefix'.filt.fastq.gz '$cleanfastq'
+	    && cp '$prefix'.contaminant.blastout '$blastout'
+	    && cp '$prefix'.blocklist '$blocklist'
+	    && cp '$prefix'.stats '$stats'
+	    ]]></command>
+    <inputs>
+	    <param name="input_file" type="data" format="bam,fastq,fastq.gz" label="Input HiFi Reads" help="HiFi reads"/>
+            <param argument="-l" name="match_length" type="integer" value="44" label="minimum length of adapter match to remove. Default=44" />
+            <param argument="-m" name="match_percentage" type="integer" value="97" label="minimum percent Match of adapter to remove. Default=97" />
+    </inputs>
+    <outputs>
+	    <data name="cleanfastq" format="fastq.gz" label="${tool.name} on ${on_string}: clean reads"/>
+	    <data name="blastout" format="tabular" label="${tool.name} on ${on_string}: contaminant blastout"/>
+            <data name="blocklist" format="txt" label="${tool.name} on ${on_string}: blocklist"/>
+	    <data name="stats" format="txt" label="${tool.name} on ${on_string}: contaminant statistic"/>
+    </outputs>
+	
+    <tests>
+	 <test>
+            <!-- #1 test with common parameters -->
+	    <param name="input_file" value="combine.fastq.gz" ftype="fastq.gz"/>
+            <param name="l" value="44" />
+	    <param name="m" value="97" />
+	    <output name="cleanfastq" file="combine.filt.fastq.gz" ftype="fastq.gz" decompress="true" />
+            <output name="blastout" file="combine.contaminant.blastout" ftype="tabular" />
+	    <output name="blocklist" file="combine.blocklist" ftype="txt" />
+        </test>
+    </tests>
+    <help><![CDATA[
+	    
+.. class:: infomark
+
+**What it does**
+	    
+*Convert .bam to .fastq and remove reads with remnant PacBio adapter sequences*
+
+**Input**
+	    
+- input file - FASTQ and BAM. Also, gipped versions of FASTQ. 
+
+**Example:**
+
+- bash pbadapterfilt.sh [ -p file Prefix ] [ -l minimum Length of adapter match to remove. Default=44 ] [ -m minimum percent Match of adapter to remove. Default=97 ] [ -t Number of threads for blastn. Default=8 ] [ -o outdirectory prefix Default=. ]
+
+**Output**
+
+- {prefix}.contaminant.blastout (Output of BLAST search)
+- {prefix}.blocklist (Headers of PB adapter contaminated reads to be removed)
+- {prefix}.filt.fastq.gz (Fastq reads free of PB adapter sequence ready for assembly)
+- {prefix}.stats (File with simple math on number of reads removed, etc)
+
+ 
+.. class:: infomark
+
+**Contributor**
+
+Galaxy Australia is the contributor wrapping the HiFiadapterFilt `Github <https://github.com/usegalaxy-au/tools-au>`_.	   
+ 
+**References**
+	    
+More information are available on `Github <https://github.com/sheinasim/HiFiAdapterFilt>`_.
+	]]></help>
+     <citations>
+	 <citation type="doi">DOI: 10.1186/s12864-022-08375-1</citation>
+     </citations>
+</tool>