--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stacks_kmerfilter.xml	Mon Jul 01 10:58:28 2019 -0400
@@ -0,0 +1,200 @@
+<tool id="stacks2_kmerfilter" name="Stacks2: kmer filter" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
+<description>Identify PCR clones</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_cmd"/>
+    <command detect_errors="aggressive"><![CDATA[
+@FASTQ_INPUT_FUNCTIONS@
+
+mkdir stacks_inputs stacks_outputs &&
+
+#set ($link_command, $fwd_path, $rev_path, $inputype) = $fastq_input_batch($input_type.fqinputs, $input_type.input_type_select)
+$link_command
+
+kmer_filter
+#if $input_type.input_type_select == 'single':
+    -f '$fwd_path'
+#else
+    -1 '$fwd_path'
+    -2 '$rev_path'
+#end if
+## TODO    $options_kmer_char.read_k_freq
+-i $inputype
+-o stacks_outputs
+$capture
+-y fastq
+$options_filtering.rare
+$options_filtering.abundant
+--k_len $options_filtering.k_len
+--max_k_freq $options_advanced_filtering.max_k_freq
+#if str($options_advanced_filtering.min_lim)!="":
+    --min_lim $options_advanced_filtering.min_lim
+#end if
+#if str($options_advanced_filtering.max_lim)!="":
+    --max_lim $options_advanced_filtering.max_lim
+#end if
+#if str($options_normalization.normalize)!="":
+    --normalize $options_normalization.normalize
+#end if
+#if $options_kmer_char.write_k_freq
+    --read_k_freq $kfreq
+#end if
+$options_kmer_char.k_dist
+#if $options_kmer_char.k_dist
+    | sed 's/KmerFrequency/# KmerFrequency/' > $kfreqdist
+#end if
+@TEE_APPEND_LOG@
+@CAT_LOG_TO_STDERR@
+
+## move outputs such that Galaxy can find them
+## if filtering is on then ...filt...fq is created
+## if normalization is on then ...norm...fq is created
+## if both are active then both files are created, but only norm is needed
+#if str($options_filtering.rare)!="" or str($options_filtering.abundant)!="" or str($options_normalization.normalize)!="":
+    #if str($options_normalization.normalize)!="":
+        #set infix="norm"
+    #else
+        #set infix="fil"
+    #end if
+    #if $capture:
+        #if $input_type.input_type_select == "single"
+            && mv stacks_outputs/*.discards.fastq '$discarded'
+        #else
+            && mv stacks_outputs/*.1.discards.fastq '$discarded_pair.forward'
+            && mv stacks_outputs/*.2.discards.fastq '$discarded_pair.reverse'
+        #end if
+    #end if
+    #if $input_type.input_type_select == "single"
+        && mv stacks_outputs/*.${infix}.fastq '$clean'
+    #else
+        && mv stacks_outputs/*.1.${infix}.fastq '$clean_pair.forward'
+        && mv stacks_outputs/*.2.${infix}.fastq '$clean_pair.reverse'
+    #end if
+#end if
+
+    ]]></command>
+    <inputs>
+        <expand macro="fastq_input_bc"/>
+        <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />
+        <section name="options_filtering" title="Filtering options" expanded="False">
+            <param argument="--rare" type="boolean" checked="false" truevalue="--rare" falsevalue="" label="Turn on filtering based on rare k-mers" />
+            <param argument="--abundant" type="boolean" checked="false" truevalue="--abundant" falsevalue="" label="Turn on filtering based on abundant k-mers" />
+            <param argument="--k_len" type="integer" value="15" label="K-mer size" />
+        </section>
+        <section name="options_advanced_filtering" title="Advanced fitering options" expanded="False">
+            <param argument="--max_k_freq" type="integer" value="20000" label="Number of times a kmer must occur to be considered abundant" />
+            <param argument="--min_lim" type="integer" value="" optional="true" label="Number of rare kmers occuring in a row required to discard a read" help="(default: 80% of the k-mer length)." />
+            <param argument="--max_lim" type="integer" value="" optional="true" label="Number of abundant kmers required to discard a read" help="(default: 80% of the k-mers in a read)" />
+        </section>
+        <section name="options_normalization" title="Normalization options" expanded="False">
+            <param argument="--normalize" type="integer" value="" optional="true" label="Normalize read depth according to k-mer coverage" />
+        </section>
+        <section name="options_kmer_char" title="Characterizing K-mers options" expanded="False">
+            <param argument="--write_k_freq" type="boolean" checked="false" truevalue="--write_k_freq" falsevalue="" label="Write kmers along with their frequency of occurrence and exit" />
+            <param argument="--k_dist" type="boolean" checked="false" truevalue="--k_dist" falsevalue="" label="Print k-mer frequency distribution and exit" />
+        </section>
+        <!--<section name="options_advanced_input" title="Advanced input options" expanded="False">
+            <param argument="\-\-read_k_freq" type="boolean" checked="false" truevalue="\-\-read_k_freq" falsevalue="" label="Read a set of kmers along with their frequencies of occurrence instead of reading raw input files" />
+        </section>-->
+        <expand macro="in_log"/>
+    </inputs>
+    <outputs>
+        <expand macro="out_log"/>
+        <data name="clean" format="fastqsanger" label="${tool.name} on ${on_string}">
+            <filter>input_type['input_type_select'] == 'single' and not options_kmer_char['k_dist']</filter>
+        </data>
+        <collection name="clean_pair" type="paired" label="${tool.name} on ${on_string}">
+            <filter>input_type['input_type_select'] == 'paired' and not options_kmer_char['k_dist']</filter>
+        </collection>
+        <data name="discarded" format="fastqsanger" label="${tool.name} on ${on_string}: discarded reads">
+            <filter>capture and input_type['input_type_select'] == 'single' and not options_kmer_char['k_dist']</filter>
+        </data>
+        <collection name="discarded_pair" type="paired" label="${tool.name} on ${on_string}: discarded reads">
+            <filter>capture and input_type['input_type_select'] == 'paired' and not options_kmer_char['k_dist']</filter>
+        </collection>
+        <data format="tabular" name="kfreq" label="${tool.name} on ${on_string} kmer frequencies">
+            <filter>options_kmer_char['write_k_freq']</filter>
+        </data>
+        <data format="tabular" name="kfreqdist" label="${tool.name} on ${on_string} kmer frequency distribution">
+            <filter>options_kmer_char['k_dist']</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- default output for filtering -->
+        <test>
+            <conditional name="input_type">
+                <param name="input_type_select" value="single" />
+                <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
+            </conditional>
+            <param name="add_log" value="yes" />
+			<output name="output_log" ftype="txt" file="kmerfilter/kmerfilter.log" lines_diff="8"/>
+            <param name="rare" value="--rare"/>
+            <param name="abundant" value="--abundant" />
+            <param name="k_len" value="16" />
+            <assert_command>
+                <has_text text="--rare" />
+                <has_text text="--abundant" />
+                <has_text text="--k_len 16" />
+            </assert_command>
+            <output name="clean" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.single.gz"/>
+        </test>
+        <test>
+            <conditional name="input_type">
+                <param name="input_type_select" value="paired" />
+                <param name="fqinputs">
+                    <collection type="paired">
+                        <element name="forward" value="clonefilter/R1_0001.1.fq.gz" />
+                        <element name="reverse" value="clonefilter/R2_0001.2.fq.gz" />
+                    </collection>
+                </param>
+            </conditional>
+            <param name="capture" value="-D" />
+            <param name="normalize" value="1" />
+            <assert_command>
+                <has_text text="--normalize 1" />
+            </assert_command>
+            <output_collection name="clean_pair" type="paired">
+                <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />
+                <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />
+            </output_collection>
+            <output_collection name="discarded_pair" type="paired">
+                <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />
+                <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />
+            </output_collection>
+        </test>
+        <!-- kfreq output -->
+        <test>
+            <conditional name="input_type">
+                <param name="input_type_select" value="single" />
+                <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
+            </conditional>
+            <section name="options_kmer_char">
+                <param name="write_k_freq" value="--write_k_freq" />
+            </section>
+            <output name="kfreq" file="kmerfilter/kfreq.tsv"/>
+        </test>
+        <!-- kfreqdist output -->
+        <test>
+            <conditional name="input_type">
+                <param name="input_type_select" value="single" />
+                <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />
+            </conditional>
+            <section name="options_kmer_char">
+                <param name="k_dist" value="--k_dist" />
+            </section>
+            <output name="kfreqdist" file="kmerfilter/kfreqdist.tsv"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+.. class:: infomark
+
+Allows paired or single-end reads to be filtered according to the number or rare or abundant kmers they contain. Useful for both RAD datasets as well as randomly sheared genomic or transcriptomic data.
+
+@STACKS_INFOS@
+]]>
+    </help>
+    <expand macro="citation" />
+</tool>