Mercurial > repos > iuc > revoluzer_crex
changeset 0:e0b7c98f29bb 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 14:29:10 +0000 |
| parents | |
| children | |
| files | crex.xml macros.xml test-data/test.fas |
| diffstat | 3 files changed, 122 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/crex.xml Tue Mar 19 14:29:10 2024 +0000 @@ -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> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Mar 19 14:29:10 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