# HG changeset patch
# User iuc
# Date 1710858536 0
# Node ID af7528402a97c957cfaf612c33067a669b8c2b43

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer commit 00e6389df9248031e385772e94a02f00719f5cba

diff -r 000000000000 -r af7528402a97 distmat.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/distmat.xml	Tue Mar 19 14:28:56 2024 +0000
@@ -0,0 +1,119 @@
+<tool id="revoluzer_distmat" name="Compute distance matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
+    <description>for gene orders</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <version_command>distmat --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        distmat
+            -f '$f'
+            $structure
+            $sign
+            $distance
+            $duplicates
+            $output_cond.output_sel
+            #if $output_cond.output_sel == ""
+                $output_cond.header
+            #end if
+            > '$out'
+    ]]></command>
+    <inputs>
+        <param argument="-f" type="data" format="fasta" label="Gene orders"/>
+        <param name="structure" type="select" label="Genome structure">
+            <option value="">Circular</option>
+            <option value="--lindir">Linear directed genomes (--lindir)</option>
+            <option value="--linund">Linear undirected genomes (--linund)</option>
+        </param>
+        <param argument="--sign" type="boolean" truevalue="--sign" falsevalue="" label="Genomes are circular"/>
+        <param name="distance" type="select" label="Distance" help="Note that the default on the old web site was to compute Breakpoint distances">
+            <option value="--crex">CREx</option>
+            <option value="">Inversion</option>
+            <option value="-b">Breakpoint</option>
+            <option value="-i -m">Common Intervals</option>
+            <option value="-i -m --lw">Length weigthed common intervals</option>
+        </param>
+        <param name="duplicates" type="select" label="Remove duplicate gene orders">
+            <option value="">No</option>
+            <option value="-d">Yes</option>
+            <option value="-D">Yes and print names of removed gene orders</option>
+        </param>
+        <conditional name="output_cond">
+            <param name="output_sel" type="select" label="Output type">
+                <option value="">Table</option>
+                <option value="--nexus">Nexus</option>
+                <option value="--list">List</option>
+            </param>
+            <when value="">
+                <param argument="--header" type="boolean" truevalue="--header" falsevalue="" label="Include header in table"/>
+            </when>
+            <when value="--nexus"/>
+            <when value="--list"/>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out" format="tabular"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="f" value="test.fas"/>
+            <output name="out">
+                <assert_contents>
+                    <has_n_lines n="5"/>
+                    <has_n_columns n="1"/> <!-- wo header 1st line is just the number of genomes -->
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="f" value="test.fas"/>
+            <param name="distance" value="Breakpoint"/>
+            <conditional name="output_cond">
+                <param name="header" value="true"/>
+            </conditional>
+            <output name="out">
+                <assert_contents>
+                    <has_n_lines n="5"/>
+                    <has_n_columns n="5"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+Usage
+.....
+
+Compute a distance matrix for gene orders of unichromosomal genomes with equal duplication free gene content,
+e.g. mitochondrial gene orders. Several distance measures are available.
+
+- CREx distance (Bernt et al 2007) all other distance measures have been implemented
+  in this software package. 
+- Inversion distance (Bergeron, Heber & Jens Stoye 2002)
+- Number of Breakpoints (e.g. Sankoff, Blanchette 1997)
+- Common Intervals (Bergeron, A., Chauve, C., de Montgolfier, F., and Raffinot, M., 2008) 
+- Conserved Intervals (Bergeron, A., Blanchette, M., Chateau, A., and Chauve, C., 2004)
+
+For the latter a distance is computed by subtracting the number from the maximum possible for the number of genes.
+
+**Input**
+
+@INPUT_FORMAT@
+
+**Output**
+
+A tabular file showing the distance matrix.
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btm468</citation>
+        <citation type="doi">10.1089/cmb.1998.5.555 </citation><!--Sankoff Blanchette-->
+        <citation type="doi">10.1093/bioinformatics/18.suppl_2.s54</citation>
+        <citation type="doi">10.1137/060651331</citation>
+        <citation type="doi">10.1007/978-3-540-30219-3_2</citation>
+    </citations>
+</tool>
\ No newline at end of file
diff -r 000000000000 -r af7528402a97 macros.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Mar 19 14:28:56 2024 +0000
@@ -0,0 +1,18 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.1.6</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <xml name="biotools">
+        <xrefs>
+            <xref type="bio.tools">revoluzer</xref>
+        </xrefs>
+    </xml>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">revoluzer</requirement>
+        </requirements>
+    </xml>
+    <token name="@INPUT_FORMAT@"><![CDATA[
+Input is a gene order FASTA file. Instead of the sequence a space separated list of gene names
+is given that may be prefixed with a minus sign to mark genes that are on the other strand.
+    ]]></token>
+</macros>
\ No newline at end of file
diff -r 000000000000 -r af7528402a97 test-data/test.fas
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.fas	Tue Mar 19 14:28:56 2024 +0000
@@ -0,0 +1,8 @@
+> genome1
+A B C D
+> genome2
+A C B D
+> genome3
+A -C -B D
+> genome4
+A -C B D
\ No newline at end of file