Initial commit of revoluzer tools

.github/CODEOWNERS

@@ -24,6 +24,7 @@
 /tools/progressivemauve/                @hexylena
 /tools/prokka/                          @nsoranzo
 /tools/raxml/                           @nsoranzo
+/tools/revoluzer/                         @bernt-matthias
 /tools/scater/                          @nsoranzo
 /tools/seurat/                          @nsoranzo
 /tools/sickle/                          @nsoranzo

tools/revoluzer/.shed.yml

@@ -0,0 +1,18 @@
+name: revoluzer
+owner: iuc
+description: revoluzer wrappers
+long_description: |
+    Gene order analysis tools
+categories:
+- Phylogenetics
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer
+homepage_url: https://gitlab.com/Bernt/revoluzer/
+type: unrestricted
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for revoluzer tool: {{ tool_name }}."
+suite:
+  name: "suite_revoluzer"
+  description: "A suite of tools that brings the revoluzer project into Galaxy."
+  long_description: |
+      Gene order analysis tools

tools/revoluzer/crex.xml

@@ -0,0 +1,96 @@
+<tool id="revoluzer_crex" name="CREx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
+    <description>reconstruct pairwise gene order rearrangement</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="biotools"/>
+    <expand macro="requirements"/>
+    <version_command>crex --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        crex 
+            -f '$f'
+            $linear
+            $method_cond.method_select
+            #if $method_cond.method_select == ""
+                $noalt
+                --wI $wI
+                --wiT $wiT
+                --wiT $wTDRL
+            #else if $method_cond.method_select == "--crex1"
+                $prinobp
+            #end if
+            > '$out'
+    ]]></command>
+    <inputs>
+        <param argument="-f" type="data" format="fasta" label="Gene orders"/>
+        <param argument="--linear" type="boolean" truevalue="--linear" falsevalue="" checked="false" label="Genomes are linear"/>
+        <conditional name="method_cond">
+            <param name="method_select" type="select" label="method">
+                <option value="">CREx2</option>
+                <option value="--crex1" selected="true">CREx1</option>
+                <option value="--bp">compute with breakpoint scenario [ZhaoBourque07]</option>
+            </param>
+            <when value="">
+                <param argument="--wI" type="float" min="0" value="1" label="Weight of an inversion"/>
+                <param argument="--wiT" type="float" min="0" value="1" label="Weight of an inverse transposition"/>
+                <param argument="--wTDRL" type="float" min="0" value="1" label="Weight of a TDRL"/>
+                <param argument="--noalt" type="boolean" truevalue="" falsevalue="--noalt" checked="true" label="Compute alternatives for T+iT"/>
+            </when>
+            <when value="--crex1">
+                <param argument="--prinobp" type="boolean" truevalue="" falsevalue="--prinobp" checked="true" label="Compute breakpoint scenario for prime nodes"/>
+            </when>
+            <when value="--bp"></when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="out" format="tabular">
+            <actions>
+                <action name="column_names" type="metadata" default="Source gene order,Target Gene order,Rearrangement,Breakpoints" />
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="f" value="test.fas"/>
+            <param name="linear" value="true"/>
+            <output name="out">
+                <metadata name="column_names" value="Source gene order,Target Gene order,Rearrangement,Breakpoints" />
+                <assert_contents>
+                    <has_n_lines n="7"/>
+                    <has_n_columns n="4"/>
+                    <has_text text="I(B C )"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+Compute rearrangement scenarios on pairs of gene orders (with equal duplication free gene content).
+
+Usage
+.....
+
+**Input**
+
+@INPUT_FORMAT@
+
+**Output**
+
+Rearrangements in the 3rd column of the outbut table are listed as follows:
+
+- I(X): the genes listed in X are inverted
+- T(X ,Y ,): The order of the gene sets X and Y is transposed
+- iT(X, Y, ): Same as transposition, but one gene of the sets is also inverted
+- TDRL(X, Y): A tandem duplication random loss where the genes in X are kept in the 1st copy and the genes in Y an the last
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1109/TCBB.2018.2831661</citation>
+        <citation type="doi">10.1093/bioinformatics/btm468</citation>
+        <citation type="doi">10.1007/978-3-540-74960-8_12</citation>
+    </citations>
+</tool>

tools/revoluzer/distmat.xml

@@ -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>

tools/revoluzer/macros.xml

@@ -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>

tools/revoluzer/test-data/test.fas

@@ -0,0 +1,8 @@
+> genome1
+A B C D
+> genome2
+A C B D
+> genome3
+A -C -B D
+> genome4
+A -C B D