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initial commit of revoluzer tools
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bernt-matthias committed Mar 15, 2024
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18 changes: 18 additions & 0 deletions tools/revoluzer/.shed.yml
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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
97 changes: 97 additions & 0 deletions tools/revoluzer/crex.xml
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<tool id="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 --verison</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"
$noalt
$prinobp
--primxalt $primxalt
#end if
> '$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="--noalt" type="boolean" truevalue="" falsevalue="--noalt" checked="true" label="Compute alternatives for T+iT"/>
<param argument="--prinobp" type="boolean" truevalue="" falsevalue="--prinobp" checked="true" label="Compute breakpoint scenario for prime nodes"/>
<param argument="--primxalt" type="integer" min="1" value="2" label="maximal number of alternatives for prime nodes (I+TDRL, bp)"></param>
</when>
<when value="--bp"></when>
</conditional>
</inputs>
<outputs>
<data name="out" format="tabular"/>
</outputs>
<tests>
<test expect_num_outputs="1">
<param name="f" value="test.fas"/>
<param name="linear" value="true"/>
<output name="out">
<assert_contents>
<has_n_lines n="6"/>
<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**
The output is a tabular file listing the 1) compared genomes, 2) the rerrangemets, 3) the affected breakpoints.
Rearrangements 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>
119 changes: 119 additions & 0 deletions tools/revoluzer/distmat.xml
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<tool id="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 --verison</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>
18 changes: 18 additions & 0 deletions tools/revoluzer/macros.xml
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<macros>
<token name="@TOOL_VERSION@">0.1.2</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>

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