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comparison cdhit_macros.xml @ 3:43724ea1c85f

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Add cd-hit for protein fastas
author Jim Johnson <jj@umn.edu>
date Thu, 27 Jun 2013 21:37:08 -0500
parents
children 28b7a43907f0
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2:cca0838c1597 3:43724ea1c85f
1 <macros>
2 <template name="common_cdhit_options">
3 <!-- start common cdhit options -->
4
5 <!-- start adv. settings -->
6 #if $advanced.settings == 'yes':
7 #if $advanced.band_width:
8 -b $advanced.band_width
9 #end if
10 #if $advanced.throw_away_len:
11 -l $advanced.throw_away_len
12 #end if
13 #if $advanced.description_len:
14 -d $advanced.description_len
15 #end if
16 #if $advanced.cutoff_diff_len:
17 -s $advanced.cutoff_diff_len
18 #end if
19 #if $advanced.aa_cutoff_diff_len:
20 -S $advanced.aa_cutoff_diff_len
21 #end if
22 #if $advanced.align.style == 'local':
23 -G 0
24 #if $advance.align.align_coverage_long:
25 -aL $advance.align.align_coverage_long
26 #end if
27 #if $advance.align.aa_align_coverage_long:
28 -AL $advance.align.aa_align_coverage_long
29 #end if
30 #if $advance.aling.align_coverage_short:
31 -aS $advance.align.align_coverage_short
32 #end if
33 #if $advance.aling.aa_align_coverage_short:
34 -AS $advance.align.aa_align_coverage_short
35 #end if
36 #if $advance.align.align_coverage_min:
37 -A $advance.align.aling_coverage_min
38 #end if
39 #end if
40 #end if
41 <!-- end adv. settings -->
42 #if $print_alignment:
43 $print_alignment
44 #end if
45 #if $cluster_type:
46 $cluster_type
47 #end if
48 </template>
49
50 <template name="runtime_tuning">
51 #if $runtime.tuning == 'tune':
52 #if $runtime.threads_num:
53 -T $runtime.threads_num
54 #end if
55 #if $runtime.memory_limit:
56 -M $runtime.memory_limit
57 #end if
58 $runtime.in_ram
59 #else
60 \$CDHIT_SITE_OPTIONS
61 #end if
62 <!-- end runtime tuning options -->
63 </template>
64
65 <macro name="common_cdhit_options">
66
67 <conditional name="advanced">
68 <param name="settings" type="select" label="Use adavanced settings">
69 <option value="no" selected="true">No</option>
70 <option value="yes">Yes</option>
71 </param>
72 <when value="no"/>
73 <when value="yes">
74 <param name="band_width" type="integer" value="" optional="true" label="band_width of alignment (default 20)">
75 <validator type="in_range" message="alignment band_width must be greater than 0" min="1"/>
76 </param>
77 <param name="throw_away_len" type="integer" value="" optional="true" label="length of throw_away_sequences (default 10)">
78 <validator type="in_range" message="throw_away_sequences length must be greater than 0" min="1"/>
79 </param>
80 <param name="description_len" type="integer" value="" optional="true" label="length of description in .clstr file (default 20)">
81 <help>if set to 0, it takes the fasta defline and stops at first space</help>
82 <validator type="in_range" message="description length cannot be negative" min="0"/>
83 </param>
84 <param name="cutoff_diff_len" type="float" value="" optional="true" label="length difference cutoff (default 0.0)">
85 <help>if set to 0.9, the shorter sequences need to be at least 90% length of the representative of the cluster</help>
86 <validator type="in_range" message="length difference cutoff must be between 0.0 and 1.0" min="0.0" max="1.0"/>
87 </param>
88 <param name="aa_cutoff_diff_len" type="integer" value="" optional="true" label="length difference cutoff in amino acid (default 999999)">
89 <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>
90 <validator type="in_range" message="length difference cutoff in amino acid be greater than 0" min="0"/>
91 </param>
92 <conditional name="align">
93 <param name="style" type="select" label="global or local alignments">
94 <help>local sequence identity, calculated as : number of identical amino acids in alignment divided by the length of the alignment
95 You must set alignment coverage by length or fraction.
96 </help>
97 <option value="global" selected="true">Global</option>
98 <option value="local" >Local</option>
99 </param>
100 <when value="global"/>
101 <when value="local">
102
103 <param name="align_coverage_long" type="float" value="" optional="true" label="alignment coverage for the longer sequence (default 0.0)">
104 <help>if set to 0.9, the alignment must covers 90% of the sequence</help>
105 <validator type="in_range" message="input must be between 0.0 and 1.0." min="0.0" max="1.0" />
106 </param>
107 <param name="aa_align_coverage_long" type="integer" value="" optional="true" label="alignment coverage control for the longer sequence (default 99999999)" >
108 <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>
109 <validator type="in_range" message="input cannot be negative." min="0" />
110 </param>
111 <param name="align_coverage_short" type="float" value="" optional="true" label="alignment coverage for the shorter sequence (default 0.0)" >
112 <help>if set to 0.9, the alignment must covers 90% of the sequence</help>
113 <validator type="in_range" message="input must be between 0.0 and 1.0." min="0.0" max="1.0" />
114 </param>
115 <param name="aa_align_coverage_short" type="integer" value="" optional="true" label="alignment coverage control for the shorter sequence (default 99999999)" >
116 <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>
117 <validator type="in_range" message="input cannot be negative." min="0" />
118 </param>
119 <param name="align_coverage_min" type="integer" value="" optional="true" label="minimal alignment coverage control for the both sequences (default 0)" >
120 <help>alignment must cover at least this value for both sequences</help>
121 <validator type="in_range" message="coverage must be at least 0." min="0"/>
122 </param>
123 </when>
124 </conditional>
125
126 </when>
127 </conditional>
128
129 <param name="print_alignment" type="boolean" truevalue="-p 1" falsevalue="" checked="false" label="Print alignment overlap in .clstr file"/>
130
131 <param name="cluster_type" type="boolean" truevalue="-g 1" falsevalue="" checked="false" label="Slow Cluster"
132 help="by cd-hit's default algorithm, a sequence is clustered to the first
133 cluster that meet the threshold (fast cluster). If set the program
134 will cluster it into the most similar cluster that meet the threshold
135 (accurate but slow mode). This won't change the representatives of final clusters"/>
136
137 </macro>
138
139 <macro name="runtime_tuning">
140 <conditional name="runtime">
141 <param name="tuning" type="select" label="Runtime Memory and Threads">
142 <option value="default" selected="true">Use Default settings</option>
143 <option value="tune" >Set Runtime options</option>
144 </param>
145 <when value="default"/>
146 <when value="tune">
147 <param name="threads_num" type="integer" value="1" optional="true" label="number of threads; with 0, all CPUs will be used. (default 1)" >
148 <validator type="in_range" message="input cannot be negative." min="0" />
149 </param>
150 <param name="memory_limit" type="integer" value="800" optional="true" label="memory limit (in MB) for the program; 0 for unlimitted. (default 800)" >
151 <validator type="in_range" message="input cannot be negative." min="0" />
152 </param>
153 <param name="in_ram" type="boolean" truevalue="-B 1" falsevalue="" checked="false" label="Too big for in Memory calculation"
154 help="Use for huge databases"/>
155 </when>
156 </conditional>
157 </macro>
158
159 <token name="@CITATION_SECTION@">------
160
161 **Citation**
162
163 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;`_
164
165 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
166
167 </token>
168 </macros>