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comparison cdhit_macros.xml @ 3:626cd6334dbc 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 12:13:50 -0400
parents aa923171e225
children ba7e9a012723
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2:aa923171e225 3:626cd6334dbc
3 <requirements> 3 <requirements>
4 <requirement type="package" version="4.6.4">cd-hit</requirement> 4 <requirement type="package" version="4.6.4">cd-hit</requirement>
5 </requirements> 5 </requirements>
6 </xml> 6 </xml>
7 7
8 <template name="common_cdhit_options"> 8 <template name="common_cdhit_options">
9 <!-- start common cdhit options --> 9 #if $advanced.settings == 'yes':
10 10
11 <!-- start adv. settings -->
12 #if $advanced.settings == 'yes':
13 #if str($advanced.band_width) != 'None': 11 #if str($advanced.band_width) != 'None':
14 -b $advanced.band_width 12 -b $advanced.band_width
15 #end if 13 #end if
14
16 #if str($advanced.throw_away_len) != 'None': 15 #if str($advanced.throw_away_len) != 'None':
17 -l $advanced.throw_away_len 16 -l $advanced.throw_away_len
18 #end if 17 #end if
18
19 #if str($advanced.description_len) != 'None': 19 #if str($advanced.description_len) != 'None':
20 -d $advanced.description_len 20 -d $advanced.description_len
21 #end if 21 #end if
22
22 #if str($advanced.cutoff_diff_len) != 'None': 23 #if str($advanced.cutoff_diff_len) != 'None':
23 -s $advanced.cutoff_diff_len 24 -s $advanced.cutoff_diff_len
24 #end if 25 #end if
26
25 #if str($advanced.aa_cutoff_diff_len) != 'None': 27 #if str($advanced.aa_cutoff_diff_len) != 'None':
26 -S $advanced.aa_cutoff_diff_len 28 -S $advanced.aa_cutoff_diff_len
27 #end if 29 #end if
30
28 #if $advanced.align.style == 'local': 31 #if $advanced.align.style == 'local':
29 -G 0 32 -G 0
30 #if str($advance.align.align_coverage_long) != 'None': 33 #if str($advance.align.align_coverage_long) != 'None':
31 -aL $advance.align.align_coverage_long 34 -aL $advance.align.align_coverage_long
32 #end if 35 #end if
33 #if str($advance.align.aa_align_coverage_long) != 'None': 36
34 -AL $advance.align.aa_align_coverage_long 37 #if str($advance.align.align_coverage_long_control) != 'None':
38 -AL $advance.align.align_coverage_long_control
35 #end if 39 #end if
40
36 #if str($advance.aling.align_coverage_short) != 'None': 41 #if str($advance.aling.align_coverage_short) != 'None':
37 -aS $advance.align.align_coverage_short 42 -aS $advance.align.align_coverage_short
38 #end if 43 #end if
39 #if str($advance.aling.aa_align_coverage_short) != 'None': 44
40 -AS $advance.align.aa_align_coverage_short 45 #if str($advance.aling.align_coverage_short_control) != 'None':
46 -AS $advance.align.align_coverage_short_control
41 #end if 47 #end if
48
42 #if str($advance.align.align_coverage_min) != 'None': 49 #if str($advance.align.align_coverage_min) != 'None':
43 -A $advance.align.aling_coverage_min 50 -A $advance.align.aling_coverage_min
44 #end if 51 #end if
45 #end if 52 #end if
46 #end if 53 #end if
47 <!-- end adv. settings --> 54
48 #if $print_alignment: 55 #if $print_alignment:
49 $print_alignment 56 $print_alignment
50 #end if 57 #end if
58
51 #if $cluster_type: 59 #if $cluster_type:
52 $cluster_type 60 $cluster_type
53 #end if 61 #end if
54 </template>
55 62
56 <template name="runtime_tuning"> 63 \$CDHIT_SITE_OPTIONS
57 #if $runtime.tuning == 'tune': 64
58 #if $runtime.threads_num: 65 -T \${GALAXY_SLOTS:-1}
59 -T $runtime.threads_num
60 #end if
61 #if $runtime.memory_limit:
62 -M $runtime.memory_limit
63 #end if
64 $runtime.in_ram
65 #else
66 \$CDHIT_SITE_OPTIONS
67 #end if
68 <!-- end runtime tuning options -->
69 </template> 66 </template>
70 67
71 <macro name="common_cdhit_options"> 68 <macro name="common_cdhit_options">
72
73 <conditional name="advanced"> 69 <conditional name="advanced">
74 <param name="settings" type="select" label="Use adavanced settings"> 70 <param name="settings" type="select" label="Use advanced settings?">
75 <option value="no" selected="true">No</option> 71 <option value="no" selected="true">No</option>
76 <option value="yes">Yes</option> 72 <option value="yes">Yes</option>
77 </param> 73 </param>
74
78 <when value="no"/> 75 <when value="no"/>
76
79 <when value="yes"> 77 <when value="yes">
80 <param name="band_width" type="integer" value="" optional="true" label="band_width of alignment (default 20)"> 78 <param name="band_width" type="integer" value="20" optional="true" label="Alignment band width" min="1" help="(-b)"/>
81 <validator type="in_range" message="alignment band_width must be greater than 0" min="1"/> 79
82 </param> 80 <param name="throw_away_len" type="integer" value="10" optional="true" label="Length of throw away sequences" min="1" help="(-l)"/>
83 <param name="throw_away_len" type="integer" value="" optional="true" label="length of throw_away_sequences (default 10)"> 81
84 <validator type="in_range" message="throw_away_sequences length must be greater than 0" min="1"/> 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)"/>
85 </param> 83
86 <param name="description_len" type="integer" value="" optional="true" label="length of description in .clstr file (default 20)"> 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)"/>
87 <help>if set to 0, it takes the fasta defline and stops at first space</help> 85
88 <validator type="in_range" message="description length cannot be negative" min="0"/> 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)"/>
89 </param> 87
90 <param name="cutoff_diff_len" type="float" value="" optional="true" label="length difference cutoff (default 0.0)">
91 <help>if set to 0.9, the shorter sequences need to be at least 90% length of the representative of the cluster</help>
92 <validator type="in_range" message="length difference cutoff must be between 0.0 and 1.0" min="0.0" max="1.0"/>
93 </param>
94 <param name="aa_cutoff_diff_len" type="integer" value="" optional="true" label="length difference cutoff in amino acid (default 999999)">
95 <help>if set to 60, the length difference between the shorter sequences and the representative of the cluster can not be bigger than 60</help>
96 <validator type="in_range" message="length difference cutoff in amino acid be greater than 0" min="0"/>
97 </param>
98 <conditional name="align"> 88 <conditional name="align">
99 <param name="style" type="select" label="global or local alignments"> 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.">
100 <help>local sequence identity, calculated as : number of identical amino acids in alignment divided by the length of the alignment
101 You must set alignment coverage by length or fraction.
102 </help>
103 <option value="global" selected="true">Global</option> 90 <option value="global" selected="true">Global</option>
104 <option value="local" >Local</option> 91 <option value="local" >Local</option>
105 </param> 92 </param>
93
106 <when value="global"/> 94 <when value="global"/>
95
107 <when value="local"> 96 <when value="local">
108 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)"/>
109 <param name="align_coverage_long" type="float" value="" optional="true" label="alignment coverage for the longer sequence (default 0.0)"> 98
110 <help>if set to 0.9, the alignment must covers 90% of the sequence</help> 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)"/>
111 <validator type="in_range" message="input must be between 0.0 and 1.0." min="0.0" max="1.0" /> 100
112 </param> 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)"/>
113 <param name="aa_align_coverage_long" type="integer" value="" optional="true" label="alignment coverage control for the longer sequence (default 99999999)" > 102
114 <help>if set to 60, and the length of the sequence is 400,then the alignment must be at least 340 (400-60) residues</help> 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)"/>
115 <validator type="in_range" message="input cannot be negative." min="0" /> 104
116 </param> 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)"/>
117 <param name="align_coverage_short" type="float" value="" optional="true" label="alignment coverage for the shorter sequence (default 0.0)" >
118 <help>if set to 0.9, the alignment must covers 90% of the sequence</help>
119 <validator type="in_range" message="input must be between 0.0 and 1.0." min="0.0" max="1.0" />
120 </param>
121 <param name="aa_align_coverage_short" type="integer" value="" optional="true" label="alignment coverage control for the shorter sequence (default 99999999)" >
122 <help>if set to 60, and the length of the sequence is 400, then the alignment must be at least 340 (400-60) residues</help>
123 <validator type="in_range" message="input cannot be negative." min="0" />
124 </param>
125 <param name="align_coverage_min" type="integer" value="" optional="true" label="minimal alignment coverage control for the both sequences (default 0)" >
126 <help>alignment must cover at least this value for both sequences</help>
127 <validator type="in_range" message="coverage must be at least 0." min="0"/>
128 </param>
129 </when> 106 </when>
130 </conditional> 107 </conditional>
131
132 </when> 108 </when>
133 </conditional> 109 </conditional>
134 110
135 <param name="print_alignment" type="boolean" truevalue="-p 1" falsevalue="" checked="false" label="Print alignment overlap in .clstr file"/> 111 <param name="print_alignment" type="boolean" truevalue="-p 1" falsevalue="" checked="false" label="Print alignment overlap in .clstr file"/>
136 112
137 <param name="cluster_type" type="boolean" truevalue="-g 1" falsevalue="" checked="false" label="Slow Cluster" 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)"/>
138 help="by cd-hit's default algorithm, a sequence is clustered to the first
139 cluster that meet the threshold (fast cluster). If set the program
140 will cluster it into the most similar cluster that meet the threshold
141 (accurate but slow mode). This won't change the representatives of final clusters"/>
142
143 </macro> 114 </macro>
144 115
145 <macro name="runtime_tuning">
146 <conditional name="runtime">
147 <param name="tuning" type="select" label="Runtime Memory and Threads">
148 <option value="default" selected="true">Use Default settings</option>
149 <option value="tune" >Set Runtime options</option>
150 </param>
151 <when value="default"/>
152 <when value="tune">
153 <param name="threads_num" type="integer" value="1" optional="true" label="number of threads; with 0, all CPUs will be used. (default 1)" >
154 <validator type="in_range" message="input cannot be negative." min="0" />
155 </param>
156 <param name="memory_limit" type="integer" value="800" optional="true" label="memory limit (in MB) for the program; 0 for unlimitted. (default 800)" >
157 <validator type="in_range" message="input cannot be negative." min="0" />
158 </param>
159 <param name="in_ram" type="boolean" truevalue="-B 1" falsevalue="" checked="false" label="Too big for in Memory calculation"
160 help="Use for huge databases"/>
161 </when>
162 </conditional>
163 </macro>
164
165 <token name="@CITATION_SECTION@">------
166
167 **Citation**
168
169 For the underlying tool, please cite `DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011 May;43(5):491-8. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21478889&gt;`_
170
171 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
172
173 </token>
174 </macros> 116 </macros>