Mercurial > repos > iuc > revoluzer_distmat
changeset 0:af7528402a97 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer commit 00e6389df9248031e385772e94a02f00719f5cba
| author | iuc |
|---|---|
| date | Tue, 19 Mar 2024 14:28:56 +0000 |
| parents | |
| children | |
| files | distmat.xml macros.xml test-data/test.fas |
| diffstat | 3 files changed, 145 insertions(+), 0 deletions(-) [+] |
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--- /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
--- /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