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comparison logol.xml @ 0:f11370aba286 draft

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planemo upload for repository https://github.com/genouest/galaxy-tools/tree/master/tools/logol commit 9ab3e793622c860adb69b1272927620abd106e73
author genouest
date Wed, 06 Jun 2018 10:35:32 -0400
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-1:000000000000 0:f11370aba286
1 <?xml version="1.0"?>
2 <tool id="logol_wrapper" name="Logol" version="1.7.8">
3 <description>Biological patterns matching</description>
4 <requirements>
5 <requirement type="package" version="1.7.8=1">logol</requirement>
6 <requirement type="package" version="6.0">unzip</requirement>
7 </requirements>
8 <command detect_errors="exit_code"><![CDATA[
9
10 ## generate properties file
11 echo -e "minSplitSize=2000000\nmaxResultSize=0\nmaxMatchSize=0\nworkingDir=.\ndir.result=.\nmaxSpacerLength=0\nmaxLength=0\nminLength=2\nparentStrategy=1\nnbProcessor=1\nnbJobs=1\nmaxSolutions=100\nminTreeIndex=2\nsuffix.tool = 2" > logol.properties
12
13 &&
14
15 LogolMultiExec.sh
16 #if str( $options_input.options_input_selector ) == "model":
17 -m ${options_input.m}
18 #else
19 -g ${options_input.g}
20 #end if
21
22 -${type}
23 -s ${s}
24 -max ${max}
25
26 ${fasta}
27 ${gff}
28 ${all}
29
30 -maxmatchsize ${maxmatchsize}
31 -maxspacer ${maxspacer}
32 -lmax ${lmax}
33 -lmin ${lmin}
34
35 ${forcesplit}
36
37 -conf logol.properties
38
39 -out 'logol_results.zip'
40
41 > ${log_file}
42
43 &&
44
45 unzip logol_results.zip
46
47 ]]></command>
48
49 <inputs>
50 <conditional name="options_input">
51 <param name="options_input_selector" type="select" label="Logol pattern type">
52 <option value="model" selected="True">Logol pattern model</option>
53 <option value="grammar">Logol pattern grammar</option>
54 </param>
55 <when value="model">
56 <param argument="-m" type="data" format="txt" label="Logol pattern model" help="Pattern model designed by LogolDesigner" />
57 </when>
58 <when value="grammar">
59 <param argument="-g" type="data" format="txt" label="Logol pattern grammar" help="Logol Grammar file" />
60 </when>
61 </conditional>
62
63 <param name="type" type="select" format="text">
64 <label>Type of personal data file</label>
65 <option value="dna">DNA</option>
66 <option value="rna">RNA</option>
67 <option value="protein">PROTEIN</option>
68 </param>
69
70 <param argument="-s" type="data" format="fasta" label="Read from file" help="Fasta sequence to analyse" />
71
72 <param argument="-max" type="integer" value="100" label="Maximum number of result matches"/>
73 <param argument="-fasta" type="boolean" truevalue="-fasta" falsevalue="" label="Add fasta conversion to result archive" checked="False" value="False"/>
74 <param argument="-gff" type="boolean" truevalue="-gff" falsevalue="" label="Add gff conversion to result archive" checked="False" value="False"/>
75 <param argument="-all" type="boolean" truevalue="-all" falsevalue="" label="Search sequence in both directions" checked="False" value="False"/>
76 <param argument="-maxmatchsize" type="integer" value="0" label="Maximum size of a match (0 is no limit)"/>
77 <param argument="-maxspacer" type="integer" value="0" label="Maximum size of a spacer (0 is no limit)"/>
78 <param argument="-lmax" type="integer" value="0" label="Maximum size of a word (0 is no limit)"/>
79 <param argument="-lmin" type="integer" value="2" label="Minimum size of a word"/>
80 <param argument="-forcesplit" truevalue="-forcesplit" falsevalue="" type="boolean" label="Allow sequence cut (if several models are defined in rule, all models will look for pattern in same sequence range" checked="False" value="False"/>
81 <param name="zip" type="boolean" label="Generate zip archive with all files" checked="False" value="False" help="Zip file contains all xml and fasta/gff files if conversion is activated"/>
82
83 </inputs>
84 <outputs>
85 <data format="txt" name="log_file" label="Log : ${tool.name} on ${on_string}" />
86 <data format="zip" name="logol_results_archive" from_work_dir="logol_results.zip" label="Compressed files : ${tool.name} on ${on_string}">
87 <filter>zip</filter>
88 </data>
89 <collection name="logol_results" type="list" label="XML files: ${tool.name} on ${on_string}">
90 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml$" ext="xml" visible="false" />
91 </collection>
92 <collection name="logol_results_gff" type="list" label="GFF files: ${tool.name} on ${on_string}">
93 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml\.gff" ext="gff" visible="false" />
94 <filter>gff</filter>
95 </collection>
96 <collection name="logol_results_fasta" type="list" label="Fasta files: ${tool.name} on ${on_string}">
97 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.xml\.fasta" ext="fasta" visible="false" />
98 <filter>fasta</filter>
99 </collection>
100 </outputs>
101 <tests>
102 <test>
103 <param name="s" value="primer.fasta" />
104 <conditional name="options_input">
105 <param name="options_input_selector" value="grammar"/>
106 <param name="g" value="primer.logol" />
107 </conditional>
108 <param name="zip" value="True" />
109 <output name="logol_results_archive" compare="sim_size" file="logol_results.zip" />
110 </test>
111 <test>
112 <param name="s" value="primer.fasta" />
113 <conditional name="options_input">
114 <param name="options_input_selector" value="grammar"/>
115 <param name="g" value="primer.logol" />
116 </conditional>
117 <param name="gff" value="True" />
118 <param name="fasta" value="True" />
119 <param name="forcesplit" value="True" />
120 <param name="all" value="True" />
121 <param name="zip" value="True" />
122 <output name="logol_results_archive" compare="sim_size" file="logol_results_multi_format.zip" />
123 </test>
124 </tests>
125
126 <help><![CDATA[
127
128 Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence (nucleic or proteic).
129
130 It includes a Linux command line tool and a graphical designer.
131
132 http://logol.genouest.org/web/app.php/logol
133
134 -------------------------------------------------------------------------
135
136 Software is free and open source, under CeCILL license
137
138
139 ]]></help>
140 <citations>
141 <citation type="doi">10.1007/978-3-319-09192-1_4</citation>
142 </citations>
143 </tool>