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comparison cmbuild.xml @ 2:fac157e22e1b draft

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author bgruening
date Fri, 13 Feb 2015 03:10:51 -0500
parents 652f9d550531
children 2c2c5e5e495b
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1:55bb96edfc07 2:fac157e22e1b
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 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). 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).
265 268
266 **Galaxy Wrapper Author**:: 269 **Galaxy Wrapper Author**::
267 270
268 * Bjoern Gruening, University of Freiburg 271 * Bjoern Gruening, University of Freiburg
269 272
273 ]]>
270 </help> 274 </help>
271 </tool> 275 </tool>