# HG changeset patch
# User galaxy-australia
# Date 1657508998 0
# Node ID bbc2060caa0e4a1cdd95fc03beb3d1836554bd2c

"planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/hifiadapter commit 1ca83d831d15156432d96f6df9e508d6c9ed09da-dirty"

diff -r 000000000000 -r bbc2060caa0e README.md
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Mon Jul 11 03:09:58 2022 +0000
@@ -0,0 +1,21 @@
+# HiFiAdapterFilt
+Remove CCS reads with remnant PacBio adapter sequences and convert outputs to a compressed .fastq (.fastq.gz).
+
+# Dependencies
+- BamTools
+- BLAST+
+
+# Installation
+Currently only tested on Ubuntu
+
+# Docker
+- HiFiAdapterFilt Docker is available on https://hub.docker.com/r/dmolik/pbadapterfilt
+
+```
+docker pull dmolik/pbadapterfilt
+docker run -t -d -v /hifireads_data_directory_on_host_machine/:/home/genomics/HiFiAdapterFilt-master/ubuntu --name hifiadapterfilt dmolik/pbadapterfilt
+docker exec -it <container_id> /bin/bash
+
+```
+
+See [official documentation](https://github.com/sheinasim/HiFiAdapterFilt) for more details.
diff -r 000000000000 -r bbc2060caa0e hifiadapterfilt.xml
--- /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>
diff -r 000000000000 -r bbc2060caa0e macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Jul 11 03:09:58 2022 +0000
@@ -0,0 +1,29 @@
+<macros>
+    <token name="@TOOL_VERSION@">2.0.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">21.05</token>
+    <token name="@DIGEST@">99b5e479baee5ffe01c676dd3d7180b0d3eb94af08db0f2ceb3641bef3ebbaa4</token>
+    <xml name="requirements">
+        <requirements>
+            <container type="docker">dmolik/pbadapterfilt:latest</container>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+      <stdio>
+         <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
+         <exit_code range="1:"  level="fatal" description="Error" />
+      </stdio>
+    </xml>	
+    <token name="@CLEAN_EXT@">
+        <![CDATA[
+        #from os.path import splitext
+        #import re
+        #def clean_ext($identifier)
+            #while $identifier.endswith(('.fq','.fastq', '.fastq.gz','.bam'))
+                #set $identifier = splitext($identifier)[0]
+            #end while
+$identifier#slurp
+        #end def
+        ]]>
+    </token>
+</macros>
diff -r 000000000000 -r bbc2060caa0e test-data/combine.blocklist
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/combine.blocklist	Mon Jul 11 03:09:58 2022 +0000
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diff -r 000000000000 -r bbc2060caa0e test-data/combine.contaminant.blastout
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/combine.contaminant.blastout	Mon Jul 11 03:09:58 2022 +0000
@@ -0,0 +1,3208 @@
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diff -r 000000000000 -r bbc2060caa0e test-data/combine.fastq.gz
Binary file test-data/combine.fastq.gz has changed
diff -r 000000000000 -r bbc2060caa0e test-data/combine.filt.fastq.gz
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