# HG changeset patch
# User thanhlv
# Date 1584566660 0
# Node ID 5127e62d11fbddf8870eefaca52b50ae92e00046
# Parent  e40d2adb0896afbf7f523b7dd9040f2108e1b88a
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/bbmap commit f832310ee25935e283f72f057790af7fad0d661b-dirty"

diff -r e40d2adb0896 -r 5127e62d11fb bbduk.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bbduk.xml	Wed Mar 18 21:24:20 2020 +0000
@@ -0,0 +1,45 @@
+<tool id="bbmap_bbduk" name="bbduk" version="@VERSION@">
+    <description> Compares reads to the kmers in a reference dataset, optionally
+allowing an edit distance</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+
+    <command detect_errors="exit_code"><![CDATA[
+        bbduk.sh
+        in1=${reads[0]} 
+        in2=${reads[1]} 
+        ref=${bbduk_adapters} 
+        out1=${pair_id}_1.trimmed.fastq.gz 
+        out2=${pair_id}_2.trimmed.fastq.gz 
+        stats=${pair_id}.stats.txt 
+        threads=${task.cpus} 
+        minlen=${params.bbduk_minlen} 
+        qtrim=${params.bbduk_qtrim} 
+        trimq=${params.bbduk_trimq} 
+        ktrim=${params.bbduk_ktrim} 
+        k=${params.bbduk_k} 
+        mink=${params.bbduk_mink} 
+        hdist=${params.bbduk_hdist} 
+        ${params.bbduk_trimbyoverlap} 
+        ${params.bbduk_trimpairsevenly}
+    ]]>    </command>
+
+    <inputs>
+        <param name="ref" type="data" format="fasta,fasta.gz" label="Reference assembly"/>
+        <param name="reads" type="data" format="fastq,fastq.gz" label="Long reads"/>
+    </inputs>
+
+    <outputs>
+        <data name="assembly" format="fasta" />
+    </outputs>
+    <help><![CDATA[
+    “Duk” stands for Decontamination Using Kmers. BBDuk was developed to combine most common data-quality-related trimming, filtering, and masking operations into a single high-performance tool. It is capable of quality-trimming and filtering, adapter-trimming, contaminant-filtering via kmer matching, sequence masking, GC-filtering, length filtering, entropy-filtering, format conversion, histogram generation, subsampling, quality-score recalibration, kmer cardinality estimation, and various other operations in a single pass. Specifically, any combination of operations is possible in a single pass, with the exception of kmer-based operations (kmer trimming, kmer masking, or kmer filtering); at most 1 kmer-based operation can be done in a single pass. BBDuk2 allows multiple kmer-based operations in a single pass, and is otherwise equivalent to BBDuk.
+
+    BBDuk’s parameters are described in its shellscript (bbduk.sh). This file provides usage examples of various common tasks.      
+    ]]>    </help>
+    <expand macro="citations" />
+
+</tool>
diff -r e40d2adb0896 -r 5127e62d11fb filter_by_name.xml
--- a/filter_by_name.xml	Thu Jan 02 17:17:56 2020 +0000
+++ b/filter_by_name.xml	Wed Mar 18 21:24:20 2020 +0000
@@ -62,6 +62,9 @@
             names=$source.name_list
         #end if
         include=$include
+        #if $q33
+            qin=33
+        #end if
         2>&1 | tee > log.txt
     ]]>    </command>
     <inputs>
@@ -94,6 +97,7 @@
                 <param name="name_list" type="data" format="txt" label="Input ID list"/>
             </when>
         </conditional>
+        <param name="q33" type="boolean" truevalue="true" falsevalue="" checked="false" label="Q33?" />
         <param name="include" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Include the filtered names" />
     </inputs>
     <outputs>