--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/obiconvert.xml	Wed Apr 12 17:39:25 2017 -0400
@@ -0,0 +1,113 @@
+<tool id="obi_convert" name="obiconvert" version="@WRAPPER_VERSION@">
+    <description>converts sequence files to different output formats</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <command>
+        <![CDATA[
+        obiconvert
+        #if $db
+            -d '$db'
+        #end if
+        #if $tax
+            -t '$tax'
+        #end if
+        ${options_inputtype}
+        ${options_seqtype}
+        --${out_format}-output
+        ${uppercase}
+        ${ecopcrdb}
+        #if str( $ecopcrdb) == "--ecopcrdb"
+            --ecopcrdb-output=${ecopcrdb_output}
+        #end if
+        '${input}' > '${output}'
+        ]]>
+
+    </command>
+
+    <inputs>
+        <param name="input" type="data" format="fastq,fasta,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)" />
+        <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database" />
+        <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/>
+        <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>
+        <param name="out_format" type="select" label="Output data type">
+            <option value="fasta" selected="true">fasta</option>
+            <option value="fastq">fastq</option>
+        </param>
+        <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?"  help="Use this option if you want to generate an ecoPCR database output file" />
+        <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue=""  label="Do you want to print sequences in upper case?" />
+
+    </inputs>
+    <outputs>
+        <data format="txt" name="ecopcrdb_output" label="result.ecopcrdb with ${tool.name} on ${on_string}">
+            <filter>ecopcrdb == True</filter>
+        </data>
+        <data format="fasta" name="output" label="output with ${tool.name} on ${on_string}" >
+            <change_format>
+                <when input="out_format" value="fastq" format="fastq" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="output_obisort.fasta" />
+            <param name="options_inputtype" value="fasta"/>
+            <param name="options_seqtype" value="--nuc"/>
+            <param name="out_format" value="fasta"/>
+            <param name="ecopcrdb" value="False"/>
+            <param name="uppercase" value="True"/>
+            <output name="output" file="output_obiconvert.fasta" ftype="fasta"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+obiconvert converts sequence files to different output formats. See the documentation for more details on the different formats.
+
+Input files can be in :
+
+fasta format
+
+extended OBITools fasta format
+
+Sanger fastq format
+
+Solexa fastq format
+
+ecoPCR format
+
+ecoPCR database format
+
+GenBank format
+
+EMBL format
+
+obiconvert converts those files to the :
+
+extended OBITools fasta format
+
+Sanger fastq format
+
+ecoPCR database format
+
+If no file name is specified, data is read from standard input.
+
+@OBITOOLS_LINK@
+
+    ]]>
+
+    </help>
+    <expand macro="citation" />
+</tool>