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comparison cdhit_macros.xml @ 0:54d811ad2b52 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/cdhit/ commit ea0424ae045ac797c080aeabab9a8536f7eb2f84-dirty
author bebatut
date Mon, 25 Apr 2016 12:15:23 -0400
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children 93f25d52cfa5
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-1:000000000000 0:54d811ad2b52
1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="4.6.4">cd-hit</requirement>
5 </requirements>
6 </xml>
7
8 <template name="common_cdhit_options">
9 #if $advanced.settings == 'yes':
10
11 #if str($advanced.band_width) != 'None':
12 -b $advanced.band_width
13 #end if
14
15 #if str($advanced.throw_away_len) != 'None':
16 -l $advanced.throw_away_len
17 #end if
18
19 #if str($advanced.description_len) != 'None':
20 -d $advanced.description_len
21 #end if
22
23 #if str($advanced.cutoff_diff_len) != 'None':
24 -s $advanced.cutoff_diff_len
25 #end if
26
27 #if str($advanced.aa_cutoff_diff_len) != 'None':
28 -S $advanced.aa_cutoff_diff_len
29 #end if
30
31 #if $advanced.align.style == 'local':
32 -G 0
33 #if str($advance.align.align_coverage_long) != 'None':
34 -aL $advance.align.align_coverage_long
35 #end if
36
37 #if str($advance.align.align_coverage_long_control) != 'None':
38 -AL $advance.align.align_coverage_long_control
39 #end if
40
41 #if str($advance.aling.align_coverage_short) != 'None':
42 -aS $advance.align.align_coverage_short
43 #end if
44
45 #if str($advance.aling.align_coverage_short_control) != 'None':
46 -AS $advance.align.align_coverage_short_control
47 #end if
48
49 #if str($advance.align.align_coverage_min) != 'None':
50 -A $advance.align.aling_coverage_min
51 #end if
52 #end if
53 #end if
54
55 #if $print_alignment:
56 $print_alignment
57 #end if
58
59 #if $cluster_type:
60 $cluster_type
61 #end if
62
63 \$CDHIT_SITE_OPTIONS
64
65 -T \${GALAXY_SLOTS:-1}
66 </template>
67
68 <macro name="common_cdhit_options">
69 <conditional name="advanced">
70 <param name="settings" type="select" label="Use advanced settings?">
71 <option value="no" selected="true">No</option>
72 <option value="yes">Yes</option>
73 </param>
74
75 <when value="no"/>
76
77 <when value="yes">
78 <param name="band_width" type="integer" value="20" optional="true" label="Alignment band width" min="1" help="(-b)"/>
79
80 <param name="throw_away_len" type="integer" value="10" optional="true" label="Length of throw away sequences" min="1" help="(-l)"/>
81
82 <param name="description_len" type="integer" value="20" optional="true" label="Length of the description" min="0" help="If set to 0, it takes the fasta defline and stops at first space (-d)"/>
83
84 <param name="cutoff_diff_len" type="float" value="0.0" optional="true" label="Length difference cutoff" min="0.0" max="1.0" help="If set to 0.9, the shorter sequences need to be at least 90% length of the representative of the cluster (-s)"/>
85
86 <param name="aa_cutoff_diff_len" type="integer" value="999999" optional="true" label="Length difference cutoff in amino acid" min="0" help="If set to 60, the length difference between the shorter sequences and the representative of the cluster can not be bigger than 60 (-S)"/>
87
88 <conditional name="align">
89 <param name="style" type="select" label="global or local alignments" help="Local sequence identity, calculated as : number of identical amino acids in alignment divided by the length of the alignment. You must set alignment coverage by length or fraction.">
90 <option value="global" selected="true">Global</option>
91 <option value="local" >Local</option>
92 </param>
93
94 <when value="global"/>
95
96 <when value="local">
97 <param name="align_coverage_long" type="float" value="0.0" optional="true" label="Alignment coverage for the longer sequence" min="0.0" max="1.0" help="If set to 0.9, the alignment must covers 90% of the sequence (-aL)"/>
98
99 <param name="align_coverage_long_control" type="integer" value="99999999" optional="true" label="Alignment coverage control for the longer sequence " min="0" help="If set to 60, and the sequence's length 400,then the alignment must be at least 340 (400-60) residues (-AL)"/>
100
101 <param name="align_coverage_short" type="float" value="0.0" optional="true" label="Alignment coverage for the shorter sequence" min="0.0" max="1.0" help="As for the longer (-aS)"/>
102
103 <param name="align_coverage_short_control" type="integer" value="99999999" optional="true" label="Alignment coverage control for the shorter sequence" min="0" help="As for the longer (-AS)"/>
104
105 <param name="align_coverage_min" type="integer" value="0" optional="true" label="Minimal alignment coverage control for the both sequences" min="0" help="Alignment must cover at least this value for both sequences (-A)"/>
106 </when>
107 </conditional>
108 </when>
109 </conditional>
110
111 <param name="print_alignment" type="boolean" truevalue="-p 1" falsevalue="" checked="false" label="Print alignment overlap in .clstr file"/>
112
113 <param name="cluster_type" type="boolean" truevalue="-g 1" falsevalue="" checked="false" label="Slow Cluster" help="In cd-hit's default algorithm, a sequence is clustered to the first cluster that meet the threshold (fast cluster). If set to slow, the program will cluster it into the most similar cluster that meet the threshold (accurate but slow mode). This won't change the representatives of final clusters (-g)"/>
114 </macro>
115
116 </macros>