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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 |
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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> |
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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> |
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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> |