--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filtlong.xml	Mon Sep 17 16:16:07 2018 -0400
@@ -0,0 +1,110 @@
+<tool id="filtlong" name="filtlong" version="0.2.0">
+    <description>Filtering long reads by quality</description>
+    <requirements>
+        <requirement type="package" version="0.2.0">filtlong</requirement>
+    </requirements>
+    <version_command>filtlong --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+filtlong
+    #if $output_thresholds.target_bases:
+        --target_bases '$output_thresholds.target_bases'
+    #end if
+    #if $output_thresholds.keep_percent:
+        --keep_percent '$output_thresholds.keep_percent'
+    #end if
+    #if $output_thresholds.min_length:
+        --min_length '$output_thresholds.min_length'
+    #end if
+    #if $output_thresholds.min_mean_q:
+        --min_mean_q '$output_thresholds.min_mean_q'
+    #end if
+    #if $output_thresholds.min_window_q:
+        --min_window_q '$output_thresholds.min_window_q'
+    #end if
+    #if $external_references.assembly:
+        --assembly '$external_references.assembly'
+    #end if
+    #if $external_references.illumina_1:
+        --illumina_1 '$external_references.illumina_1'
+    #end if
+    #if $external_references.illumina_2:
+        --illumina_2 '$external_references.illumina_2'
+    #end if
+    --length_weight '$score_weights.length_weight'
+    --mean_q_weight '$score_weights.mean_q_weight'
+    --window_q_weight '$score_weights.window_q_weight'
+    $read_manipulation.trim
+    #if $read_manipulation.split:
+        --split '$read_manipulation.split'
+    #end if
+    #if $other.window_size:
+        --window_size '$other.window_size'
+    #end if
+    '$input_file' > output.fastq
+    ]]></command>
+    <inputs>
+        <param name="input_file" type="data" format="fastq" label="Input FASTQ" help="FASTQ of input reads"/>
+        <section name="output_thresholds" title="Output thresholds">
+            <param argument="--target_bases" type="integer" min="0" optional="True" label="Total bases" help="Keep only the best reads up to this many total bases"/>
+            <param argument="--keep_percent" type="float" min="0" max="100" optional="True" label="Keep percentage" help="Keep only this percentage of the best reads (measured by bases)"/>
+            <param argument="--min_length" type="integer" min="0" optional="True" label="Min. length" help="Minimum length threshold"/>
+            <param argument="--min_mean_q" type="float" min="0" optional="True" label="Min. mean quality" help="Minimum mean quality threshold"/>
+            <param argument="--min_window_q" type="float" min="0" optional="True" label="Min. window quality" help="Minimum window quality threshold"/>
+        </section>
+        <section name="external_references" title="External references">
+            <param argument="--assembly" type="data" format="fasta" optional="True" label="Reference assembly" help="Reference assembly in FASTA format"/>
+            <param argument="--illumina_1" type="data" format="fastq,fastq.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
+            <param argument="--illumina_2" type="data" format="fastq,fastq.gz" optional="True" label="Reference Illumina read" help="Reference Illumina reads in FASTQ format"/>
+        </section>
+        <section name="score_weights" title="Score weights">
+            <param argument="--length_weight" type="float" min="0" value="1" optional="True" label="Weight length score" help="Weight given to the length score (default: 1)"/>
+            <param argument="--mean_q_weight" type="float" min="0" value="1" optional="True" label="Weight mean quality" help="Weight given to the mean quality score (default: 1)"/>
+            <param argument="--window_q_weight" type="float" min="0" value="1" optional="True" label="Weight window quality" help="Weight given to the window quality score (default: 1)"/>
+        </section>
+        <section name="read_manipulation" title="Read manipulation">
+            <param argument="--trim" type="boolean" checked="false" truevalue="--trim" falsevalue="" label="Trim non-k-mer-matching" help="Trim non-k-mer-matching bases from start/end of reads"/>
+            <param argument="--split" type="integer" min="0" optional="True" label="Split at nr. of bases" help="split reads at this many (or more) consecutive non-k-mer-matching bases"/>
+        </section>
+        <section name="other" title="Other">
+            <param argument="--window_size" type="integer" min="0" value="250" optional="True" label="Sliding window size" help="size of sliding window used when measuring window quality (default: 250)"/>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="fastq" from_work_dir="output.fastq" label="${tool.name} on ${on_string}: Filtered FASTQ"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="fastq" value="test.fastq"/>
+            <param name="min_length" value="1000"/>
+            <param name="keep_percent" value="50"/>
+            <param name="target_bases" value="500000000"/>
+            <output name="outfile" ftype="fastq" file="output.fastq"/>
+        </test>
+        <test>
+            <param name="input_file" ftype="fastq" value="test_reference.fasta"/>
+            <param name="illumina_1" ftype="fastq.gz" value="test_reference_1.fastq.gz"/>
+            <param name="illumina_2" ftype="fastq.gz" value="test_reference_2.fastq.gz"/>
+            <param name="min_length" value="1000"/>
+            <param name="keep_percent" value="90"/>
+            <param name="target_bases" value="500000000"/>
+            <param name="trim" value="True"/>
+            <param name="split" value="500"/>
+            <output name="outfile" ftype="fastq" file="output_reference.fastq"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @misc{rrwick2017,
+                author = {Wick, Ryan},
+                year = {2017},
+                title = {Filtlong},
+                publisher = {GitHub},
+                journal = {GitHub repository},
+                url = {https://github.com/rrwick/Filtlong},
+            }
+        </citation>
+    </citations>
+</tool>