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comparison gblocks.xml @ 0:daf61c79c8b4 draft

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks commit 2c1d4da58bb81f0b7232a1b3f0b3a0fde752de33
author earlhaminst
date Thu, 12 Apr 2018 06:59:23 -0400
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children 40191026adfd
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-1:000000000000 0:daf61c79c8b4
1 <tool id="gblocks" name="Gblocks" version="0.91b">
2 <description>Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis</description>
3 <requirements>
4 <requirement type="package" version="0.91b">gblocks</requirement>
5 </requirements>
6 <command><![CDATA[
7 ln -s '$inputFile' input.pir && Gblocks
8 input.pir
9 -t=$t
10 #if $advanced.a == '-a'
11 #if str($advanced.b1)
12 -b1=$advanced.b1
13 #end if
14 #if str($advanced.b2)
15 -b2=$advanced.b2
16 #end if
17 -b3=$advanced.b3
18 -b4=$advanced.b4
19 -b5=$advanced.b5
20 -b6=$advanced.b6
21 -b0=$advanced.b0
22 #end if
23 #set $output_opt = ''
24 #if $outputs
25 #set $outputs_arr = str($outputs).split(',')
26 #for $o in $outputs_arr
27 #set $output_opt += $o + '=y '
28 #end for
29 #else
30 #set $outputs_arr = []
31 #end if
32 #if $output_opt
33 #set $output_opt = $output_opt[:-1]
34 #end if
35 $output_opt
36 > '$outputFile'
37 ]]></command>
38 <inputs>
39 <param name="inputFile" type="data" format="fasta,pir" label="Multiple Sequence Alignment" help="Multiple Sequence Alignment in Fasta format." />
40 <param argument="-t" type="select" label="Type Of Sequence">
41 <option value="p" selected="true">Protein</option>
42 <option value="d">DNA</option>
43 <option value="c">Codons</option>
44 </param>
45 <conditional name="advanced">
46 <param name="a" type="select" label="Specify Advanced Parameters">
47 <option value="-a">Yes</option>
48 <option value="" selected="true">No</option>
49 </param>
50 <when value="" />
51 <when value="-a">
52 <param argument="-b1" type="integer" min="1" value="" optional="true" label="Minimum number of sequences for a conserved position" help="Any integer bigger than half the number of sequences and smaller or equal than the total number of sequences" />
53 <param argument="-b2" type="integer" min="1" value="" optional="true" label="Minimum number of sequences for a flank position" help="Any integer equal or bigger than minimum number of sequences for a conserved position" />
54 <param argument="-b3" type="integer" value="8" label="Maximum number of contiguous nonconserved positions" />
55 <param argument="-b4" type="integer" value="10" min="2" label="Minimum length of a block" />
56 <param argument="-b5" type="select" label="Allowed gap positions">
57 <option value="n" selected="true">None</option>
58 <option value="h">With Half</option>
59 <option value="a">All</option>
60 </param>
61 <param argument="-b6" type="select" label="Use similarity matrices">
62 <option value="y" selected="true">Yes</option>
63 <option value="n">No</option>
64 </param>
65 <param argument="-b0" type="integer" value="10" min="2" label="Minimum length of an intial block" />
66 </when>
67 </conditional>
68 <param name="outputs" type="select" multiple="true" optional="true" display="checkboxes" label="Output formats">
69 <option value="-s" selected="true">Selected blocks</option>
70 <option value="-p" selected="true">Results and parameters File</option>
71 <option value="-n">Nonconserved blocks</option>
72 <option value="-u">Ungapped alignment</option>
73 <option value="-k">Mask file with the selected blocks</option>
74 <option value="-d">Postscript file with the selected blocks</option>
75 </param>
76 </inputs>
77 <outputs>
78 <data name="outputFile" format="txt" label="${tool.name} on ${on_string}" />
79 <data name="Results_and_parameters_file" format="html" from_work_dir="input.pir-gb.htm" label="${tool.name} Results and parameters on ${on_string}" >
80 <filter>outputs and '-p' in outputs</filter>
81 </data>
82 <data name="Selected_blocks" format="txt" from_work_dir="input.pir-gb" label="${tool.name} Selected blocks on ${on_string}" >
83 <filter>outputs and '-s' in outputs</filter>
84 </data>
85 <data name="Nonconserved_blocks" format="txt" from_work_dir="input.pir-gbComp" label="${tool.name} Nonconserved blocks on ${on_string}" >
86 <filter>outputs and '-n' in outputs</filter>
87 </data>
88 <data name="Ungapped_alignment" format="txt" from_work_dir="input.pir--" label="${tool.name} Ungapped alignment on ${on_string}" >
89 <filter>outputs and '-u' in outputs</filter>
90 </data>
91 <data name="Masked_file_with_the_selected_blocks" format="txt" from_work_dir="input.pir-gbMask" label="${tool.name} Masked file with the selected blocks on ${on_string}" >
92 <filter>outputs and '-k' in outputs</filter>
93 </data>
94 <data name="Postscript_file_with_the_selected_blocks" format="eps" from_work_dir="input.pir-gbPS" label="${tool.name} Postscript on ${on_string}" >
95 <filter>outputs and '-d' in outputs</filter>
96 </data>
97 </outputs>
98 <tests>
99 <test>
100 <param name="inputFile" ftype="fasta" value="nad3.fasta" />
101 <param name="-t" value="p" />
102 <param name="outputs" value="-s,-p" />
103 <output name="outputFile" file="Gblocks_on_data_95.txt" />
104 <output name="Results_and_parameters_file" file="Gblocks_Results_And_Parameters_on_data_95_html.html" />
105 <output name="Selected_blocks" file="Gblocks_Selected_Blocks_on_data_95.txt" />
106 </test>
107 <test>
108 <param name="inputFile" ftype="fasta" value="nad3.fasta" />
109 <param name="-t" value="p" />
110 <param name="outputs" value="-s" />
111 <output name="outputFile" file="Gblocks_on_data_95.txt" />
112 <output name="Selected_blocks" file="Gblocks_Selected_Blocks_on_data_95.txt" />
113 </test>
114 </tests>
115 <help><![CDATA[
116 Simple wrapper for `Gblocks`_. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.
117
118 .. _Gblocks: http://molevol.cmima.csic.es/castresana/Gblocks.html
119 ]]></help>
120 <citations>
121 <citation type="doi">10.1093/oxfordjournals.molbev.a026334</citation>
122 </citations>
123 </tool>