--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/presto_collapseseq.xml	Wed May 30 15:36:25 2018 -0400
@@ -0,0 +1,93 @@
+<tool id="presto_collapseseq" name="pRESTO CollapseSeq" version="@PRESTO_VERSION@">
+    <description>Remove/collapse duplicate sequences</description>
+    
+    <macros>
+        <import>presto_macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements"/>
+    
+    <version_command>CollapseSeq.py --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$fastq_in' in.fastq &&
+        CollapseSeq.py
+          -s in.fastq
+          -n '$n'
+          --uf $uf
+          --cf $cf
+          --act $act
+          $inner
+          $keepmiss
+          
+          #if $representative.select_by == "by_min"
+            --minf '$minf'
+          #end if
+          #if $representative.select_by == "by_max"
+            --maxf '$maxf'
+          #end if
+
+          --outname=tmp 
+          #if $capture_log
+            --log '$log_out'
+          #end if
+    ]]></command>
+
+    <inputs>
+        <param argument="-s" name="fastq_in" type="data" format="fastq"
+            label="Input FASTQ file" help="FASTQ file of sequences."/>
+        <param argument="-n" type="integer" value="0" label="Max Missing" 
+            help="Maximum number of missing nucleotides to consider for collapsing sequences. A sequence will be considered undetermined if it contains too many missing nucleotides."/>
+        <param argument="--uf" type="text" value="" label="Unique Field(s)" help="Space-separated list of fields to match reads by."/>
+        <param argument="--cf" type="text" value="" label="Copy Field(s)" help="Space-separated list of fields to copy into the target sequence headers.">
+            <expand macro="text-regex-validator"/>
+        </param>
+        <param argument="--act" type="text" value="" label="Action(s)" help="Space-separated list of actions to take on Copy Field(s).">
+            <expand macro="text-regex-validator"/>
+        </param>
+        <param argument="--inner" type="boolean" value="false" truevalue="--inner" falsevalue="" label="Inner" help="If true, trim off any missing/undetermined bases from the ends of reads after collapsing."/>
+        <param argument="--keepmiss" type="boolean" value="false" truevalue="--keepmiss" falsevalue="" label="Keep Missing" 
+            help="If specified, sequences with more missing characters than the threshold set by the -n parameter will be written to the unique sequence output file with a DUPCOUNT=1 annotation. If not specified, such sequences will be written to a separate file."/>
+        <conditional name="representative">
+            <param name="select_by" type="select">
+                <option value="first">First Sequence</option>
+                <option value="by_min">By field minimum value</option>
+                <option value="by_max">By field maximum value</option>
+            </param>
+            <when value="first"></when>
+            <when value="by_min">
+                <param argument="--minf" type="text" value="" label="Field Name" help="Specifies the field whose minimum value determines the retained sequence."/>
+            </when>
+            <when value="by_max">
+                <param argument="--maxf" type="text" value="" label="Field Name" help="Specifies the field whose maximum value determines the retained sequence."/>
+            </when>
+        </conditional>
+        <expand macro="presto-log-param"/>
+    </inputs>
+
+    <outputs>
+        <data name="fastq_out" format="fastq" from_work_dir="tmp_collapse-unique.fastq"/>
+        <expand macro="presto-log-output"/>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="fastq_in" value="presto_collapseseq_test_in.fastq"/>
+            <param name="n" value="0"/>
+            <param name="uf" value="PRCONS CREGION"/>
+            <param name="cf" value="CONSCOUNT"/>
+            <param name="act" value="sum"/>
+            <param name="inner" value="true"/>
+            <param name="keepmiss" value="true"/>
+            <output name="fastq_out" file="presto_collapseseq_test_output.fastq" sort="true"/>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+Removes/collapses duplicate sequences from FASTQ files.
+
+See the `pRESTO online help <@PRESTO_URL_BASE@/CollapseSeq.html>`_ for more information.
+
+@HELP_NOTE@
+    ]]></help>
+    <expand macro="citations" />
+</tool>