--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/stacks_shortreads.xml	Mon Jul 01 11:02:39 2019 -0400
@@ -0,0 +1,163 @@
+<!-- this is essentially a copy of stacks_procrad minus the unsupported options -->
+<tool id="stacks2_shortreads" name="Stacks2: process shortreads" profile="@PROFILE@" version="@STACKS_VERSION@+galaxy@WRAPPER_VERSION@">
+<description>fast cleaning of randomly sheared genomic or transcriptomic data</description>
+    <macros>
+        <import>macros.xml</import>
+        <import>macros_process.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, $inputype) = $fastq_input_nonbatch( $input_type.fqinputs, $input_type.input_type_select, "_R%d_0" )
+$link_command
+
+
+process_shortreads
+
+@PROCESS_IOOPTIONS@
+@PROCESS_FILTER@
+@COMMON_ADVANCED@
+@RESCUE_BARCODE@
+@PROCESS_ADAPTER@
+
+## advanced options not shared between shortreads and radtags
+$options_advanced.no_read_trimming
+$options_advanced.mate_pair
+$options_advanced.no_overhang
+
+#if $output_log
+    && mv stacks_outputs/process_shortreads.log $output_log
+#end if
+@PROCESS_FASTQ_POSTPROC@
+    ]]></command>
+
+    <inputs>
+        <expand macro="fastq_input_bc_file" multiple="true" listtype="list:paired"/>
+        <section name="options_advanced" title="advanced options" expanded="False">
+            <expand macro="common_advanced"/>
+            <param argument="--no_read_trimming" type="boolean" checked="false" truevalue="--no_read_trimming" falsevalue="" label="Do not trim low quality reads, just discard them" />
+            <param argument="--mate-pair" name="mate_pair" type="boolean" checked="false" truevalue="--mate-pair" falsevalue="" label="Raw reads are circularized mate-pair data, first read will be reverse complemented" />
+            <param argument="--no_overhang" type="boolean" checked="false" truevalue="--no_overhang" falsevalue="" label="Data does not contain an overhang nucleotide between barcode and seqeunce" />
+            <expand macro="rescue_barcode"/>
+            <expand macro="process_adapter"/>
+        </section>
+        <expand macro="process_filter"/>
+        <expand macro="process_output_types"/>
+    </inputs>
+
+    <outputs>
+        <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file" from_work_dir="stacks_outputs/process_shortreads.log" />
+        <expand macro="process_outputs"/>
+    </outputs>
+
+    <tests>
+        <!-- test single end, default options -->
+        <test>
+            <param name="input_type|input_type_select" value="single"/>
+            <param name="input_type|fqinputs" ftype="fastqsanger" value="procrad/R1.fq"/>
+            <param name="input_type|barcode_encoding" value="--inline_null"/>
+            <param name="barcode" value="procrad/barcodes"/>
+            <param name="add_log" value="yes" />
+            <output name="output_log" file="shortreads/process_shortreads.out" lines_diff="4"/>
+            <output_collection name="demultiplexed" count="40">
+                <element name="PopA_01" file="shortreads/PopA_01.fq" ftype="fastqsanger" />
+            </output_collection>
+        </test>
+        <!-- test single end, default options -->
+        <test>
+            <param name="input_type|input_type_select" value="paired"/>
+            <param name="input_type|fqinputs">
+                <collection type="list:paired">
+                    <element name="reads">
+                        <collection type="paired">
+                            <element name="forward" value="procrad/R1.fq" ftype="fastqsanger" />
+                            <element name="reverse" value="procrad/R2.fq" ftype="fastqsanger"/>
+                        </collection>
+                    </element>
+                </collection>
+            </param>
+            <param name="input_type|barcode_encoding" value="--inline_null"/>
+            <param name="barcode" value="procrad/barcodes"/>
+            <param name="capture" value="true"/>
+            <param name="no_read_trimming" value="--no_read_trimming" />
+            <param name="mate_pair" value="--mate-pair" />
+            <param name="no_overhang" value="--no_overhang" />
+            <param name="outype" value="gzfastq"/>
+            <param name="add_log" value="yes" />
+            <assert_command>
+                <has_text text="--no_read_trimming" />
+                <has_text text="--mate-pair" />
+                <has_text text="--no_overhang" />
+            </assert_command>
+            <output name="output_log" file="shortreads/process_shortreads.out" compare="sim_size"/>
+            <output_collection name="demultiplexed_paired" type="list:paired" count="40">
+                <element name="PopA_01">
+                    <element name="forward" value="shortreads/PopA_01.forward.fq.gz" ftype="fastqsanger.gz" compare="sim_size"/>
+                    <element name="reverse" value="shortreads/PopA_01.reverse.fq.gz" ftype="fastqsanger.gz" compare="sim_size"/>
+                </element>
+            </output_collection>
+            <output_collection name="remaining" type="list:paired" count="40">
+                <element name="PopA_01">
+                    <element name="forward" file="shortreads/PopA_01.rem.forward.fq.gz" ftype="fastqsanger.gz"/>
+                    <element name="reverse" file="shortreads/PopA_01.rem.reverse.fq.gz" ftype="fastqsanger.gz"/>
+                </element>
+            </output_collection>
+            <output_collection name="discarded_paired" type="list:paired" count="1">
+                <element name="reads">
+                    <element name="forward" file="shortreads/reads.forward.fq" ftype="fastqsanger"/>
+                    <element name="reverse" file="shortreads/reads.forward.fq" ftype="fastqsanger"/>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+.. class:: infomark
+
+**What it does**
+
+Performs the same task as process_radtags for fast cleaning of randomly sheared genomic or transcriptomic data, not for RAD data.
+
+**Help**
+
+Input files:
+
+- FASTQ
+
+- Barcode File Format
+
+The barcode file is a very simple format:
+
+======= ===========
+Barcode Sample name
+======= ===========
+ATGGGG  PopA_01
+GGGTAA  PopA_02
+AGGAAA  PopA_03
+TTTAAG  PopA_04
+GGTGTG  PopA_05
+TGATGT  PopA_06
+======= ===========
+
+Combinatorial barcodes are specified, one per column, separated by a tab:
+
+======== ======== ===========
+Barcode1 Barcode2 Sample name
+======== ======== ===========
+CGATA    ACGTA    PopA_01
+CGGCG    CGTA     PopA_02
+GAAGC    CGTA     PopA_03
+GAGAT    CGTA     PopA_04
+CGATA    AGCA     PopA_05
+CGGCG    AGCA     PopA_06
+======== ======== ===========
+
+@STACKS_INFOS@
+]]>
+    </help>
+    <expand macro="citation" />
+</tool>