--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/presto_filterseq.xml	Wed May 30 15:36:41 2018 -0400
@@ -0,0 +1,127 @@
+<tool id="presto_filterseq" name="pRESTO FilterSeq" version="@PRESTO_VERSION@">
+    <description>Filters and/or masks reads based on length, quality, missing bases and repeats.</description>
+    
+    <macros>
+        <import>presto_macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements"/>
+    
+    <version_command>FilterSeq.py --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$fastq_in' in.fastq &&
+        FilterSeq.py '$cc.command'
+          --nproc "\${GALAXY_SLOTS:-1}"
+          -s in.fastq
+          #if $varExists('cc.q')
+            -q '$cc.q'
+          #end if
+          #if $getVar('cc.inner', False)
+            --inner
+          #end if
+          #if $varExists('cc.win')
+            --win '$cc.win'
+          #end if
+          #if $getVar('cc.reverse', False)
+            --reverse
+          #end if
+          #if $varExists('cc.n')
+            -n '$cc.n'
+          #end if
+          --outdir=.
+          --outname=tmp_filter_seq 
+          #if $capture_log
+            --log '$log_out'
+          #end if
+          &&
+        mv ./tmp_filter_seq_${cc.command}-pass.fastq $fastq_out
+    ]]></command>
+    <inputs>
+        <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file"/>
+        <conditional name="cc">
+            <param name="command" type="select" label="Command">
+                <option value="length">Filters reads by length (length)</option>
+                <option value="missing">Filters reads by N or gap character count (missing)</option>
+                <option value="repeats">Filters reads by consecutive nucleotide repeats (repeats)</option>
+                <option value="quality">Filters reads by quality score (quality)</option>
+                <option value="maskqual">Masks low quality positions (maskqual)</option>
+                <option value="trimqual">Trims sequences by quality score decay (trimqual)</option>
+            </param>
+            <when value="length">
+                <param argument="-n" type="integer" value="" label="Minimum Length" help="Discard reads shorter than this number of bases long."/>
+            </when>
+            <when value="missing">
+                <param argument="-n" type="integer" value="" label="Max Missing" help="Dicard reads with more than this many no-calls or gaps."/>
+            </when>
+            <when value="repeats">
+                <param argument="-n" type="integer" value="" label="Max Repeat Length" help="Discard reads with simple repeats of this length of longer."/>
+            </when>
+            <when value="quality">
+                <param argument="-q"  type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/>
+                <param argument="--inner" type="boolean" value="false" label="End-Trim Ns" help="Exclude Ns at the ends of the reads from calculation."/>
+            </when>
+            <when value="maskqual">
+                <param argument="-q" type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/>
+            </when>
+            <when value="trimqual">
+                <param argument="-q" type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/>
+                <param argument="--win" type="integer" value="10" label="Window Size" help="Window size for moving average quality calculation."/>
+                <param argument="--reverse" type="boolean" value="false" label="Reverse" help="If true trim the start of the reads instead of the ends."/>
+            </when>
+        </conditional>
+        <expand macro="presto-log-param"/>
+    </inputs>
+
+    <outputs>
+        <data name="fastq_out" format="fastq"/>
+        <expand macro="presto-log-output"/>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param  name="command" value="length"/>
+            <param  name="n" value="299"/>
+            <param  name="fastq_in" value="presto_filterseq_test_in.fastq"/>
+            <output name="fastq_out" file="presto_filterseq_length_test_out.fastq" sort="true"/>
+        </test>
+        <test>
+            <param  name="command" value="missing"/>
+            <param  name="n" value="281"/>
+            <param  name="fastq_in" value="presto_filterseq_test_in.fastq"/>
+            <output name="fastq_out" file="presto_filterseq_missing_test_out.fastq" sort="true"/>
+        </test>
+        <test>
+            <param  name="command" value="repeats"/>
+            <param  name="n" value="8"/>
+            <param  name="fastq_in" value="presto_filterseq_test_in.fastq"/>
+            <output name="fastq_out" file="presto_filterseq_repeats_test_out.fastq" sort="true"/>
+        </test>
+        <test>
+            <param  name="command" value="quality"/>
+            <param  name="q" value="30"/>
+            <param  name="fastq_in" value="presto_filterseq_test_in.fastq"/>
+            <output name="fastq_out" file="presto_filterseq_quality_test_out.fastq" sort="true"/>
+        </test>
+        <test>
+            <param  name="command" value="maskqual"/>
+            <param  name="q" value="30"/>
+            <param  name="fastq_in" value="presto_filterseq_test_in.fastq"/>
+            <output name="fastq_out" file="presto_filterseq_maskqual_test_out.fastq" sort="true"/>
+        </test>
+        <test>
+            <param  name="command" value="trimqual"/>
+            <param  name="q" value="30"/>
+            <param  name="fastq_in" value="presto_filterseq_test_in.fastq"/>
+            <output name="fastq_out" file="presto_filterseq_trimqual_test_out.fastq" sort="true"/>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+Filters and/or masks reads based on length, quality, missing bases and repeats.
+
+See the `pRESTO online help <@PRESTO_URL_BASE@/FilterSeq.html>`_ for more information.
+
+@HELP_NOTE@
+    ]]></help>
+    <expand macro="citations" />
+</tool>