--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/read_extractor.xml	Fri Dec 03 23:10:39 2021 +0000
@@ -0,0 +1,104 @@
+<tool id="megan_read_extractor" name="MEGAN: Extract reads" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>by classification</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#set input_identifier = 'input.' + $input.ext.upper()
+ln -s '${input}' '${input_identifier}' &&
+
+read-extractor 
+--input '${input_identifier}'
+#if $frameShiftCorrect:
+    --frameShiftCorrect '$frameShiftCorrect'
+#end if
+#if str($specify_classification_cond.specify_classification) == 'yes':
+    --classification '$specify_classification_cond.classification'
+    #if str($specify_classification_cond.specify_classification) == 'yes':
+        #if $specify_classification_cond.classNames:
+            --classNames '$specify_classification_cond.classNames'
+        #end if
+    #end if
+#else:
+    --all
+#end if
+#if $ignoreExceptions:
+    --ignoreExceptions '$ignoreExceptions'
+#end if
+--gzipOutputFiles 'false'
+## Output must be a directory.
+--output ./output.txt
+&& mv ./output.txt '${output}'
+]]></command>
+    <inputs>
+        <param name="input" argument="--input" type="data" format="daa,rma6" label="Input file"/>
+        <param argument="--frameShiftCorrect" type="boolean" truevalue="true" falsevalue="" checked="false" label="Extract frame-shift corrected reads?" help="Set to Yes only if blast mode of input is BlastX"/>
+        <conditional name="specify_classification_cond">
+            <param name="specify_classification" type="select" label="Specify classification to use?">
+                <option value="yes" selected="true">Yes</option>
+                <option value="no">No</option>
+            </param>
+            <when value="yes">
+                <param argument="--classification" type="select" label="Select classification to use">
+                    <expand macro="classification_options"/>
+                </param>
+                <param argument="--classNames" type="text" value="" label="Names (or ids) of classes from which to extract reads" help="Leave blank to extract all classes">
+                    <expand macro="sanitize_query" validinitial="string.ascii_letters,string.punctuation"/>
+                </param>
+            </when>
+            <when value="no"/>
+        </conditional>
+
+        <param argument="--ignoreExceptions" type="boolean" truevalue="true" falsevalue="" checked="false" label="Ignore exceptions and continue processing?"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="txt"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input" value="read_extractor_input.rma6" ftype="rma6"/>
+            <param name="specify_classification" value="no"/>
+            <output name="output" file="read_extractor_output.txt" ftype="txt"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="read_extractor_input.rma6" ftype="rma6"/>
+            <param name="classification" value="Taxonomy"/>
+            <param name="ignoreExceptions" value="true"/>
+            <output name="output" ftype="txt">
+                <assert_contents>
+                    <has_size value="0"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_failure="true">
+            <param name="input" value="read_extractor_input.rma6" ftype="rma6"/>
+            <param name="classification" value="EGGNOG"/>
+            <assert_stderr>
+                <has_text text="Input file does not contain the requested classification 'EGGNOG'"/>
+            </assert_stderr>
+        </test>
+        <test expect_failure="true">
+            <param name="input" value="read_extractor_input.rma6" ftype="rma6"/>
+            <param name="frameShiftCorrect" value="true"/>
+            <param name="specify_classification" value="no"/>
+            <assert_stderr>
+                <has_text text="Frame-shift correction only possible when BlastMode is BLASTX"/>
+            </assert_stderr>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Extracts reads from a DAA or RMA file by classification.  This tool accepts the following input data formats.
+
+ * **Direct Access Archive (DAA)** - a proprietary file format developed by PowerISO Computing for disk image files
+ * RealMedia Audio (RMA)** - a proprietary multimedia container format created by RealNetworks.  MEGAN uses an update of the original RMA file format known as RMA6 which requires less disk space for files.
+
+This tool outputs a text file containing the reads.
+
+    </help>
+    <expand macro="citations"/>
+</tool>
+