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comparison cmbuild.xml @ 13:ffa96097e5b2 draft

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author bgruening
date Fri, 13 Feb 2015 03:12:04 -0500
parents c17ed5a530d2
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12:c17ed5a530d2 13:ffa96097e5b2
2 <description>from sequence alignments (cmbuild)</description> 2 <description>from sequence alignments (cmbuild)</description>
3 <parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" shared_inputs="" merge_outputs="cmfile_outfile"></parallelism> 3 <parallelism method="multi" split_inputs="alignment_infile" split_mode="to_size" split_size="10" shared_inputs="" merge_outputs="cmfile_outfile"></parallelism>
4 <requirements> 4 <requirements>
5 <requirement type="package">infernal</requirement> 5 <requirement type="package">infernal</requirement>
6 <requirement type="package" version="1.1">infernal</requirement> 6 <requirement type="package" version="1.1">infernal</requirement>
7 <requirement type="package" version="8.21">gnu_coreutils</requirement> 7 <requirement type="package" version="8.22">gnu_coreutils</requirement>
8 </requirements> 8 </requirements>
9 <command> 9 <command>
10 cmbuild 10 <![CDATA[
11 cmbuild
11 #if $is_summery_output: 12 #if $is_summery_output:
12 -o $summary_outfile 13 -o $summary_outfile
13 #end if 14 #end if
14 15
15 ## to many outputs, is that one really needed? 16 ## to many outputs, is that one really needed?
16 ##-O $annotated_source_alignment_outfile 17 ##-O $annotated_source_alignment_outfile
17 18
18 $model_construction_opts.model_construction_opts_selector 19 $model_construction_opts.model_construction_opts_selector
19 #if $model_construction_opts.model_construction_opts_selector == '--fast': 20 #if $model_construction_opts.model_construction_opts_selector == '--fast':
53 $cyk 54 $cyk
54 #end if 55 #end if
55 56
56 $cmfile_outfile 57 $cmfile_outfile
57 $alignment_infile 58 $alignment_infile
58 59
60 ]]>
59 </command> 61 </command>
60 <inputs> 62 <inputs>
61 <!-- Stockholm or SELEX 63 <!-- Stockholm or SELEX
62 SELEX is defined in EMBOSS datatypes 64 SELEX is defined in EMBOSS datatypes
63 --> 65 -->
64 <param name="alignment_infile" type="data" format="stockholm,selex" label="Sequence database"/> 66 <param name="alignment_infile" type="data" format="stockholm,selex" label="Sequence database"/>
65 67
66 <conditional name="model_construction_opts"> 68 <conditional name="model_construction_opts">
67 <param name="model_construction_opts_selector" type="select" label="These options control how consensus columns are defined in an alignment" help=""> 69 <param name="model_construction_opts_selector" type="select" label="These options control how consensus columns are defined in an alignment" help="">
68 <option value="--fast" selected="true">automatic (--fast)</option> 70 <option value="--fast" selected="true">automatic (--fast)</option>
69 <option value="--hand">user defined (--hand)</option> 71 <option value="--hand">user defined (--hand)</option>
70 </param> 72 </param>
71 <when value="--fast"> 73 <when value="--fast">
72 <param name="symfrac" type="float" value="0.5" size="5" 74 <param name="symfrac" type="float" value="0.5" size="5"
73 label="Define the residue fraction threshold necessary to define a consensus (--symfrac)" help=""/> 75 label="Define the residue fraction threshold necessary to define a consensus (--symfrac)" help=""/>
74 </when> 76 </when>
75 <when value="--hand"/> 77 <when value="--hand"/>
76 </conditional> 78 </conditional>
77 79
78 <param name="noss" truevalue="--noss" falsevalue="" checked="False" type="boolean" 80 <param name="noss" truevalue="--noss" falsevalue="" checked="False" type="boolean"
79 label="Ignore the secondary structure annotation, if any, in your multiple alignment file (--noss)" help=""/> 81 label="Ignore the secondary structure annotation, if any, in your multiple alignment file (--noss)" help=""/>
80 82
81 <conditional name="relative_weights_opts"> 83 <conditional name="relative_weights_opts">
82 <param name="relative_weights_opts_selector" type="select" label="Options controlling relative weights" help=""> 84 <param name="relative_weights_opts_selector" type="select" label="Options controlling relative weights" help="">
83 <option value="--wpb" selected="true">Henikoff (--wgb)</option> 85 <option value="--wpb" selected="true">Henikoff (--wgb)</option>
89 <when value="--wpb"/> 91 <when value="--wpb"/>
90 <when value="--wgsc"/> 92 <when value="--wgsc"/>
91 <when value="--wnone"/> 93 <when value="--wnone"/>
92 <when value="--wgiven"/> 94 <when value="--wgiven"/>
93 <when value="--wblosum"> 95 <when value="--wblosum">
94 <param name="wid" type="float" value="0.5" size="5" 96 <param name="wid" type="float" value="0.5" size="5"
95 label="Percent identity for clustering the alignment (--wid)" help=""/> 97 label="Percent identity for clustering the alignment (--wid)" help=""/>
96 </when> 98 </when>
97 </conditional> 99 </conditional>
98 100
99 101
102 <option value="--eent" selected="true">entropy weighting strategy (--eent)</option> 104 <option value="--eent" selected="true">entropy weighting strategy (--eent)</option>
103 <option value="--enone">Turn off the entropy weighting strategy (--enone)</option> 105 <option value="--enone">Turn off the entropy weighting strategy (--enone)</option>
104 </param> 106 </param>
105 <when value="--enone"/> 107 <when value="--enone"/>
106 <when value="--eent"> 108 <when value="--eent">
107 <param name="ere" type="float" value="0.59" size="5" 109 <param name="ere" type="float" value="0.59" size="5"
108 label="Set the target mean match state relative entropy (--ere)" help=""/> 110 label="Set the target mean match state relative entropy (--ere)" help=""/>
109 111
110 <param name="eminseq" type="integer" value="" size="5" 112 <param name="eminseq" type="integer" value="" size="5"
111 label="Define the minimum allowed effective sequence number (--eminseq)" help=""/> 113 label="Define the minimum allowed effective sequence number (--eminseq)" help=""/>
112 114
113 <param name="ehmmre" type="float" value="" size="5" 115 <param name="ehmmre" type="float" value="" size="5"
114 label="Set the target HMM mean match state relative entropy (--ehmmre)" help=""/> 116 label="Set the target HMM mean match state relative entropy (--ehmmre)" help=""/>
115 117
116 <param name="eset" type="integer" value="" size="5" 118 <param name="eset" type="integer" value="" size="5"
117 label="Set the effective sequence number for entropy weighting (--eset)" help=""/> 119 label="Set the effective sequence number for entropy weighting (--eset)" help=""/>
118 </when> 120 </when>
119 </conditional> 121 </conditional>
120 122
121 123
136 <when value="--gibbs"> 138 <when value="--gibbs">
137 <param name="random_seed" type="integer" value="0" label="Randam Seed" help="" /> 139 <param name="random_seed" type="integer" value="0" label="Randam Seed" help="" />
138 </when> 140 </when>
139 </conditional> 141 </conditional>
140 142
141 <param name="l" truevalue="-l" falsevalue="" checked="False" type="boolean" 143 <param name="l" truevalue="-l" falsevalue="" checked="False" type="boolean"
142 label="Turn on the local alignment algorithm" help="... which allows the alignment to span two or more subsequences if necessary"/> 144 label="Turn on the local alignment algorithm" help="... which allows the alignment to span two or more subsequences if necessary"/>
143 145
144 <param name="notrunc" truevalue="--notrunc" falsevalue="" checked="False" type="boolean" 146 <param name="notrunc" truevalue="--notrunc" falsevalue="" checked="False" type="boolean"
145 label="Turn off the truncated alignment algorithm" help=""/> 147 label="Turn off the truncated alignment algorithm" help=""/>
146 148
147 <param name="cyk" type="select" label="Options for refining the input alignment" help=""> 149 <param name="cyk" type="select" label="Options for refining the input alignment" help="">
148 <option value="" selected="true">optimal accuracy algorithm</option> 150 <option value="" selected="true">optimal accuracy algorithm</option>
149 <option value="--cyk">align with the CYK algorithm</option> 151 <option value="--cyk">align with the CYK algorithm</option>
150 </param> 152 </param>
151 153
152 <param name="refine_output" truevalue="" falsevalue="" checked="False" type="boolean" 154 <param name="refine_output" truevalue="" falsevalue="" checked="False" type="boolean"
153 label="Output the refined alignment file as it is used to build the covariance model" help=""/> 155 label="Output the refined alignment file as it is used to build the covariance model" help=""/>
154 156
155 </when> 157 </when>
156 </conditional> 158 </conditional>
157 159
158 160
159 <param name="is_summery_output" truevalue="" falsevalue="" checked="False" type="boolean" 161 <param name="is_summery_output" truevalue="" falsevalue="" checked="False" type="boolean"
160 label="Output a summery file?" help=""/> 162 label="Output a summery file?" help=""/>
161 163
162 </inputs> 164 </inputs>
163 <outputs> 165 <outputs>
164 166
177 </filter> 179 </filter>
178 </data> 180 </data>
179 181
180 </outputs> 182 </outputs>
181 <help> 183 <help>
184 <![CDATA[
182 185
183 186
184 **What it does** 187 **What it does**
185 188
186 For each multiple sequence alignment build a covariance model. 189 For each multiple sequence alignment build a covariance model.
259 262
260 263
261 How do I cite Infernal? 264 How do I cite Infernal?
262 ----------------------- 265 -----------------------
263 266
264 The Infernal 1.0 paper (Nawrocki et al., 2009) is the best paper to reference. 267 The recommended citation for using Infernal 1.1 is E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches , Bioinformatics 29:2933-2935 (2013).
265 If you’re writing for an enlightened (url-friendly) journal, you may want to cite the webpage
266 http://infernal.janelia.org/ because it is kept up-to-date. We hope to publish a paper related to
267 Infernal version 1.1 soon.
268 268
269 **Galaxy Wrapper Author**:: 269 **Galaxy Wrapper Author**::
270 270
271 * Bjoern Gruening, University of Freiburg 271 * Bjoern Gruening, University of Freiburg
272 272
273 ]]>
273 </help> 274 </help>
274 </tool> 275 </tool>