--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/presto_parseheaders.xml	Wed May 30 15:36:08 2018 -0400
@@ -0,0 +1,176 @@
+<tool id="presto_parseheaders" name="pRESTO ParseHeaders" version="@PRESTO_VERSION@">
+    <description>Manage annotations in FASTQ headers.</description>
+    
+    <macros>
+        <import>presto_macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements"/>
+    
+    <version_command>ParseHeaders.py --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$fastq_in' in.fastq &&
+        ParseHeaders.py $cc.command
+          -s in.fastq
+          
+          #if $varExists('cc.f')
+            -f $cc.f
+          #end if
+          #if $varExists('cc.u')
+            -u $cc.u
+          #end if
+          #if $varExists('cc.act')
+            --act $cc.act
+          #end if
+          #if $varExists('cc.k')
+            -k $cc.k
+          #end if
+
+          --outdir=.
+          --outname=tmp &&
+        mv ./tmp_*header* '$output'
+    ]]></command>
+
+    <inputs>
+        <param name="fastq_in" type="data" format="fastq" label="Input FASTQ file"/>
+
+        <conditional name="cc">
+            <param name="command" type="select" label="Command">
+                <option value="add">Add field/value pairs to header annotations (add)</option>
+                <option value="collapse">Collapse header annotations with multiple entries (collapse)</option>
+                <option value="copy">Copy header annotation fields (copy)</option>
+                <option value="delete">Delete fields from header annotations (delete)</option>
+                <option value="expand">Expand annotation fields with multiple values (expand)</option>
+                <option value="rename">Rename header annotation fields (rename)</option>
+                <option value="table">Write sequence headers to a table (table)</option>
+            </param>
+            <when value="add">
+                <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to add.">
+                    <expand macro="text-regex-validator"/>
+                </param>
+                <param argument="-u" type="text" value="" label="Value(s)" help="Space-separated list of values, one per field.">
+                    <expand macro="text-regex-validator"/>
+                </param>
+            </when>
+            <when value="collapse">
+                <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to collapse values within.">
+                    <expand macro="text-regex-validator"/>
+                </param>
+                <param argument="--act" type="text" value="" label="Action(s)" help="Space-separated list of actions, one per field [min,max,sum,first,last,set,cat].">
+                    <expand macro="text-regex-validator"/>
+                </param>
+            </when>
+            <when value="copy">
+                <param argument="-f" type="text" value="" label="Source Field(s)" help="Space-separated list of field names to copy.">
+                    <expand macro="text-regex-validator"/>
+                </param>
+                <param argument="-k" type="text" value="" label="Target Field(s)" help="Space-separated list of target field names, one per source field.">
+                    <expand macro="text-regex-validator"/>
+                </param>
+                <param argument="--act" type="text" value="" label="Action(s)" help="Space-separated list of actions, one per target field [min,max,sum,first,last,set,cat].">
+                    <expand macro="text-regex-validator"/>
+                </param>
+            </when>
+            <when value="delete">
+                <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to delete.">
+                    <expand macro="text-regex-validator"/>
+                </param>
+            </when>
+            <when value="expand">
+                <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to expand.">
+                    <expand macro="text-regex-validator"/>
+                </param>
+            </when>
+            <when value="rename">
+                <param argument="-f" type="text" value="" label="Source Field(s)" help="Space-separated list of field names to rename.">
+                    <expand macro="text-regex-validator"/>
+                </param>
+                <param argument="-k" type="text" value="" label="Target Field(s)" help="Space-separated list of new field names.">
+                    <expand macro="text-regex-validator"/>
+                </param>
+                <param argument="--act" type="text" value="" label="Action(s)" help="Space-separated list of actions, one per new field [min,max,sum,first,last,set,cat].">
+                    <expand macro="text-regex-validator"/>
+                </param>
+            </when>
+            <when value="table">
+                <param argument="-f" type="text" value="" label="Field(s)" help="Space-separated list of field names to report on.">
+                    <expand macro="text-regex-validator"/>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="fastq">
+            <change_format>
+                <when input="command" value="table" format="tsv"/>
+            </change_format>
+        </data>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param  name="command" value="add"/>
+            <param  name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
+            <param  name="f" value="FOO BAR"/>
+            <param  name="u" value="hello world"/>
+            <output name="output" file="presto_parseheaders_test_add_out.fastq" sort="true"/>
+        </test>
+        
+        <test>
+            <param  name="command" value="collapse"/>
+            <param  name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
+            <param  name="f" value="CONSCOUNT"/>
+            <param  name="act" value="sum"/>
+            <output name="output" file="presto_parseheaders_test_collapse_out.fastq" sort="true"/>
+        </test>
+
+        <test>
+            <param  name="command"  value="copy"/>
+            <param  name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
+            <param  name="f" value="PRCONS"/>
+            <param  name="k" value="PRIMER"/>
+            <param  name="act" value="set"/>
+            <output name="output" file="presto_parseheaders_test_copy_out.fastq" sort="true"/>
+        </test>
+
+        <test>
+            <param  name="command" value="delete"/>
+            <param  name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
+            <param  name="f" value="CONSCOUNT SEQORIENT"/>
+            <output name="output" file="presto_parseheaders_test_delete_out.fastq" sort="true"/>
+        </test>
+
+        <test>
+            <param  name="command" value="expand"/>
+            <param  name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
+            <param  name="f" value="CONSCOUNT"/>
+            <output name="output" file="presto_parseheaders_test_expand_out.fastq" sort="true"/>
+        </test>
+        
+        <test>
+            <param  name="command" value="rename"/>
+            <param  name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
+            <param  name="f" value="PRCONS"/>
+            <param  name="k" value="PRIMER"/>
+            <param  name="act" value="set"/>
+            <output name="output" file="presto_parseheaders_test_rename_out.fastq" sort="true"/>
+        </test>
+
+        <test>
+            <param  name="command" value="table"/>
+            <param  name="fastq_in" value="presto_parseheaders_test_in.fastq"/>
+            <param  name="f" value="PRCONS PRIMER"/>
+            <output name="output" file="presto_parseheaders_test_table_out.tsv" sort="true"/>
+        </test>
+    </tests>
+    
+    <help><![CDATA[
+Adds, removes, renames and otherwise transforms annotations in FASTQ headers.
+
+See the `pRESTO online help <@PRESTO_URL_BASE@/ParseHeaders.html>`_ for more information.
+
+@HELP_NOTE@
+    ]]></help>
+    <expand macro="citations" />
+</tool>