Mercurial > repos > earlhaminst > gblocks
comparison gblocks.xml @ 0:daf61c79c8b4 draft default tip
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/gblocks commit 2c1d4da58bb81f0b7232a1b3f0b3a0fde752de33
author | earlhaminst |
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date | Thu, 12 Apr 2018 06:59:23 -0400 |
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-1:000000000000 | 0:daf61c79c8b4 |
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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> |