--- a/obitab.xml	Thu Nov 28 15:50:25 2019 -0500
+++ b/obitab.xml	Mon May 10 19:35:19 2021 +0000
@@ -1,66 +1,53 @@
-<tool id="obi_tab" name="obitab" version="@TOOL_VERSION@">
-    <description>converts sequence file to a tabular file that can be open by a spreadsheet program or R</description>
-    <macros>
-        <import>macros.xml</import>
-    </macros>
-    <expand macro="requirements"/>
-    <expand macro="stdio"/>
-
-    <command>
-
-        <![CDATA[
-        obitab
-        #if $additional_file
-            --omit-attribute='$additional_file'
-        #end if
-        ${output_seq_option}
-        ${no_definition_option}
-        ${options_inputtype}
-        ${options_seqtype}
-
-        '$input' > '$output'
-        ]]>
-
-    </command>
-
-    <inputs>
-        <param name="input" type="data" format="fastq,fasta,txt,tabular" label="Input sequences file" />
-        <param name="output_seq_option" type="boolean" checked="false" truevalue="-o" falsevalue="" label="Do you want to add an extra column?" help="Use this option if you want to add an extra column at the end of the table for the sequence itself"/>
-        <param name="no_definition_option" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Do you want to remove column containing the sequence definition?" help="Use this option if you want to remove column containing the sequence definition in the output tab file"/>
-        <param name="additional_file" type="data" optional="true" format="tabular" label="filter attributes from tabular file" />
-        <param name="options_inputtype" type="select" label="Specify the input datatype">
-            <expand macro="inputtype"/>
-        </param>
-        <param name="options_seqtype" type="select" label="Specify the sequence datatype" >
-            <option value="--nuc" selected="true">nucleic</option>
-            <option value="--prot">protein</option>
-        </param>
-    </inputs>
-    <outputs>
-        <data format="tabular" name="output" label="output.tabular with ${tool.name} on ${on_string}" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="input" value="output_obisort.fastq" />
-            <param name="output_seq_option" value="False"/>
-            <param name="no_definition_option" value="True"/>
-            <param name="options_inputtype" value="fasta"/>
-            <param name="options_seqtype" value="--prot"/>
-            <output name="output" file="output_obitab.txt" ftype="tabular"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-
-
-.. class:: infomark
-
-**What it does**
-
-obitab command converts sequence file to a tabular file that can be open by a spreadsheet program or R
-
-@OBITOOLS_LINK@
-
-    ]]>
-    </help>
-    <expand macro="citation" />
-    </tool>
+<tool id="obi_tab" name="obitab" version="@TOOL_VERSION@" profile="@PROFILE@">
+    <description>converts sequence file to a tabular file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <command><![CDATA[
+        @GUNZIP_INPUT@
+        
+        obitab
+        --without-progress-bar
+        #if $additional_file
+            --omit-attribute='$additional_file'
+        #end if
+        ${output_seq_option}
+        ${no_definition_option}
+        @INPUT_FORMAT@
+        input > '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" />
+        <param name="output_seq_option" type="boolean" checked="false" truevalue="-o" falsevalue="" label="Do you want to add an extra column?" help="Use this option if you want to add an extra column at the end of the table for the sequence itself"/>
+        <param name="no_definition_option" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Do you want to remove column containing the sequence definition?" help="Use this option if you want to remove column containing the sequence definition in the output tab file"/>
+        <param name="additional_file" type="data" optional="true" format="tabular" label="filter attributes from tabular file" />
+        <expand macro="input_format_options_macro"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="output_obisort.fastq" />
+            <param name="output_seq_option" value="False"/>
+            <param name="no_definition_option" value="True"/>
+            <output name="output" file="output_obitab.txt" ftype="tabular"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+
+.. class:: infomark
+
+**What it does**
+
+obitab command converts sequence file to a tabular file that can be open by a spreadsheet program or R
+
+@OBITOOLS_LINK@
+
+    ]]>
+    </help>
+    <expand macro="citation" />
+</tool>
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