--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/maf-convert.xml	Wed Jun 17 14:50:21 2020 -0400
@@ -0,0 +1,143 @@
+<tool id="last_maf_convert" name="MAF-convert" version="@LAST_CONDA_VERSION@+galaxy0" profile="18.01">
+
+    <description>read MAF-format alignments and write them in another format.</description>
+
+    <macros>
+        <import>macros_last.xml</import>
+    </macros>
+
+    <requirements>
+        <requirement type="package" version="@LAST_CONDA_VERSION@">last</requirement>
+    </requirements>
+
+    <command detect_errors="exit_code"><![CDATA[
+        maf-convert
+
+        $maf_convert.output_type.output_format 
+
+        $maf_convert.noheader
+
+        #if $maf_convert.output_type.output_format == 'psl'
+            $maf_convert.output_type.protein 
+            -j $maf_convert.output_type.j
+        #end if
+
+        #if $maf_convert.output_type.output_format == 'sam'
+            $maf_convert.output_type.sam_file.dictionary
+            #if $maf_convert.output_type.sam_file.dictionary == '-d'
+                -f $maf_convert.output_type.sam_file.f
+            #end if
+            #if $maf_convert.output_type.readfile != ''
+                -r $maf_convert.output_type.r
+            #end if
+        #end if
+
+        #if $maf_convert.output_type.output_format == 'blast' or $maf_convert.output_type.output_format == 'html'
+            -l $maf_convert.output_type.l
+        #end if
+
+        '$maf_file'
+
+        > '$outfile'
+
+    ]]></command>
+    <inputs>
+        <param name="maf_file" type="data" format="maf" label="MAF file to convert" />
+
+        <section name="maf_convert" title="MAF-convert arguments" expanded="true">
+
+            <param name="noheader" argument="-n" type="boolean" truevalue="-n" falsevalue="" checked="false" label="No header." help="Omit any header lines from the output"/>
+
+            <conditional name="output_type">
+                <param name="output_format" type="select" multiple="false" label="Output format">
+                    <option value="axt">axt</option>
+                    <option value="blast">blast</option>
+                    <option value="blasttab">blasttab</option>
+                    <option value="chain">chain</option>
+                    <option value="html">html</option>
+                    <option value="psl" selected="true">psl</option>
+                    <option value="sam">sam</option>
+                    <option value="tab">tab</option>
+                </param>
+                <when value="blast">
+                    <param argument="-l" type="integer" value="60" label="Line length"/>
+                </when>
+                <when value="html">
+                    <param argument="-l" type="integer" value="60" label="Line length"/>
+                </when>
+                <when value="psl">
+                    <param name="protein" argument="-p" type="boolean" truevalue="-p" falsevalue="" checked="false" label="Protein alignments." />
+                    <param argument="-j" type="integer" value="1" label="Join neighboring alignments" help="Join neighboring alignments if they are co-linear and separated by at most N letters."/>
+                </when>
+                <when value="sam">
+                    <conditional name="sam_file">
+                        <param name="dictionary" argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false" label="Include dictionary of sequence lengths in sam format"/>
+                        <when value="-d">
+                            <param argument="-f" type="data" format="dict" label="Get a sequence dictionary from DICTFILE" />
+                        </when>
+                    </conditional>			    
+                    <param argument="-r" type="text" value="" label="Specify read group information" help="Example: 'ID:1 PL:ILLUMINA SM:mysample'"/>
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+
+    <outputs>
+        <data format="maf" name="outfile" label="${on_string} to ${maf_convert.output_type.output_format}">
+            <change_format>
+                <when input="maf_convert.output_type.output_format" value="axt" format="axt" />
+                <when input="maf_convert.output_type.output_format" value="blast" format="blastxml" />
+                <when input="maf_convert.output_type.output_format" value="blasttab" format="blastxml" />
+                <when input="maf_convert.output_type.output_format" value="chain" format="txt" />
+                <when input="maf_convert.output_type.output_format" value="html" format="html" />
+                <when input="maf_convert.output_type.output_format" value="psl" format="tabular" />
+                <when input="maf_convert.output_type.output_format" value="sam" format="sam" />
+                <when input="maf_convert.output_type.output_format" value="tab" format="tabular" />
+            </change_format>
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/>
+            <section name="maf_convert">
+                <conditional name="output_type">
+                    <param name="output_format" value="axt"/>
+                </conditional>
+            </section>
+            <output name="outfile" file="outfile_convert.axt"/>
+        </test>
+        <test>
+            <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/>
+            <section name="maf_convert">
+                <conditional name="output_type">
+                    <param name="output_format" value="blast"/>
+                </conditional>
+            </section>
+            <output name="outfile" file="outfile_convert.blast"/>
+        </test>
+        <test>
+            <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/>
+            <section name="maf_convert">
+                <conditional name="output_type">
+                    <param name="output_format" value="html"/>
+                </conditional>
+            </section>
+            <output name="outfile" file="outfile_convert.html"/>
+        </test>
+        <test>
+            <param name="maf_file" value="last_align_train_gen.maf" ftype="maf"/>
+            <section name="maf_convert">
+                <conditional name="output_type">
+                    <param name="output_format" value="tab"/>
+                </conditional>
+            </section>
+            <output name="outfile" file="outfile_convert.tab"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+        This script reads alignments in maf format, and writes them in another format. It can write them in these formats: axt, blast, blasttab, chain, html, psl, sam, tab.
+    ]]></help>
+    <citations><expand macro="citations"/></citations>
+</tool>