Mercurial > repos > iuc > revoluzer_crex
comparison crex.xml @ 0:e0b7c98f29bb draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/revoluzer commit 00e6389df9248031e385772e94a02f00719f5cba
author | iuc |
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date | Tue, 19 Mar 2024 14:29:10 +0000 |
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1 <tool id="revoluzer_crex" name="CREx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT"> | |
2 <description>reconstruct pairwise gene order rearrangement</description> | |
3 <macros> | |
4 <import>macros.xml</import> | |
5 </macros> | |
6 <expand macro="biotools"/> | |
7 <expand macro="requirements"/> | |
8 <version_command>crex --version</version_command> | |
9 <command detect_errors="exit_code"><![CDATA[ | |
10 crex | |
11 -f '$f' | |
12 $linear | |
13 $method_cond.method_select | |
14 #if $method_cond.method_select == "" | |
15 $noalt | |
16 --wI $wI | |
17 --wiT $wiT | |
18 --wiT $wTDRL | |
19 #else if $method_cond.method_select == "--crex1" | |
20 $prinobp | |
21 #end if | |
22 > '$out' | |
23 ]]></command> | |
24 <inputs> | |
25 <param argument="-f" type="data" format="fasta" label="Gene orders"/> | |
26 <param argument="--linear" type="boolean" truevalue="--linear" falsevalue="" checked="false" label="Genomes are linear"/> | |
27 <conditional name="method_cond"> | |
28 <param name="method_select" type="select" label="method"> | |
29 <option value="">CREx2</option> | |
30 <option value="--crex1" selected="true">CREx1</option> | |
31 <option value="--bp">compute with breakpoint scenario [ZhaoBourque07]</option> | |
32 </param> | |
33 <when value=""> | |
34 <param argument="--wI" type="float" min="0" value="1" label="Weight of an inversion"/> | |
35 <param argument="--wiT" type="float" min="0" value="1" label="Weight of an inverse transposition"/> | |
36 <param argument="--wTDRL" type="float" min="0" value="1" label="Weight of a TDRL"/> | |
37 <param argument="--noalt" type="boolean" truevalue="" falsevalue="--noalt" checked="true" label="Compute alternatives for T+iT"/> | |
38 </when> | |
39 <when value="--crex1"> | |
40 <param argument="--prinobp" type="boolean" truevalue="" falsevalue="--prinobp" checked="true" label="Compute breakpoint scenario for prime nodes"/> | |
41 </when> | |
42 <when value="--bp"></when> | |
43 </conditional> | |
44 </inputs> | |
45 <outputs> | |
46 <data name="out" format="tabular"> | |
47 <actions> | |
48 <action name="column_names" type="metadata" default="Source gene order,Target Gene order,Rearrangement,Breakpoints" /> | |
49 </actions> | |
50 </data> | |
51 </outputs> | |
52 <tests> | |
53 <test expect_num_outputs="1"> | |
54 <param name="f" value="test.fas"/> | |
55 <param name="linear" value="true"/> | |
56 <output name="out"> | |
57 <metadata name="column_names" value="Source gene order,Target Gene order,Rearrangement,Breakpoints" /> | |
58 <assert_contents> | |
59 <has_n_lines n="7"/> | |
60 <has_n_columns n="4"/> | |
61 <has_text text="I(B C )"/> | |
62 </assert_contents> | |
63 </output> | |
64 </test> | |
65 </tests> | |
66 <help><![CDATA[ | |
67 | |
68 .. class:: infomark | |
69 | |
70 **What it does** | |
71 | |
72 Compute rearrangement scenarios on pairs of gene orders (with equal duplication free gene content). | |
73 | |
74 Usage | |
75 ..... | |
76 | |
77 **Input** | |
78 | |
79 @INPUT_FORMAT@ | |
80 | |
81 **Output** | |
82 | |
83 Rearrangements in the 3rd column of the outbut table are listed as follows: | |
84 | |
85 - I(X): the genes listed in X are inverted | |
86 - T(X ,Y ,): The order of the gene sets X and Y is transposed | |
87 - iT(X, Y, ): Same as transposition, but one gene of the sets is also inverted | |
88 - 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 | |
89 | |
90 ]]></help> | |
91 <citations> | |
92 <citation type="doi">10.1109/TCBB.2018.2831661</citation> | |
93 <citation type="doi">10.1093/bioinformatics/btm468</citation> | |
94 <citation type="doi">10.1007/978-3-540-74960-8_12</citation> | |
95 </citations> | |
96 </tool> |