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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
author bgruening
date Mon, 11 Nov 2024 10:27:19 +0000
parents c9e29ac5d099
children
comparison
equal deleted inserted replaced
8:c9e29ac5d099 9:1d74ed49cf41
2 <description>Search covariance model(s) against a sequence database </description> 2 <description>Search covariance model(s) against a sequence database </description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <!--parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="500" merge_outputs="outfile,multiple_alignment_output"></parallelism--> 6 <!--parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="500" merge_outputs="outfile,multiple_alignment_output"></parallelism-->
7 <expand macro="xrefs"/>
7 <expand macro="requirements"/> 8 <expand macro="requirements"/>
8 <expand macro="stdio" /> 9 <expand macro="stdio" />
9 <expand macro="xrefs"/>
10 <command> 10 <command>
11 <![CDATA[ 11 <![CDATA[
12 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy 12 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
13 ## it will be converted to a tab delimited file and piped to Galaxy 13 ## it will be converted to a tab delimited file and piped to Galaxy
14 temp_tabular_output=\$(mktemp) && 14 temp_tabular_output=\$(mktemp) &&
37 -Z $Z 37 -Z $Z
38 #end if 38 #end if
39 #if $A: 39 #if $A:
40 $A '$multiple_alignment_output' 40 $A '$multiple_alignment_output'
41 #end if 41 #end if
42 $noali
43 $verbose
42 #if str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incE": 44 #if str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incE":
43 --incE $inclusion_thresholds_opts.incE 45 --incE $inclusion_thresholds_opts.incE
44 #elif str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incT": 46 #elif str($inclusion_thresholds_opts.inclusion_thresholds_selector) == "--incT":
45 --incT $inclusion_thresholds_opts.incT 47 --incT $inclusion_thresholds_opts.incT
46 #end if 48 #end if
77 ]]> 79 ]]>
78 </command> 80 </command>
79 <inputs> 81 <inputs>
80 82
81 <param name="seqdb" type="data" format="fasta" label="Sequence database"/> 83 <param name="seqdb" type="data" format="fasta" label="Sequence database"/>
82 84 <expand macro="DB" />
83 <conditional name="cm_opts">
84 <param name="cm_opts_selector" type="select" label="Subject covariance models">
85 <option value="db" selected="True">Locally installed covariance models</option>
86 <option value="histdb">Covariance model from your history</option>
87 </param>
88 <when value="db">
89 <param name="database" type="select" label="Covariance models">
90 <options from_file="infernal.loc">
91 <column name="value" index="0"/>
92 <column name="name" index="1"/>
93 <column name="path" index="2"/>
94 </options>
95 </param>
96 </when>
97 <when value="histdb">
98 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
99 </when>
100 </conditional>
101 85
102 <param argument="-g" truevalue="-g" falsevalue="" checked="False" type="boolean" 86 <param argument="-g" truevalue="-g" falsevalue="" checked="False" type="boolean"
103 label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/> 87 label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/>
104 <param argument="-Z" type="float" min="0" optional="true" label="Calculate E-values as if the search space size is 'x' megabases (Mb)" help=""/> 88 <param argument="-Z" type="float" min="0" optional="true" label="Calculate E-values as if the search space size is 'x' megabases (Mb)" help=""/>
105 89
239 <filter>A is True</filter> 223 <filter>A is True</filter>
240 </data> 224 </data>
241 225
242 </outputs> 226 </outputs>
243 <tests> 227 <tests>
244 <test> 228 <test expect_num_outputs="1">
245 <conditional name="cm_opts"> 229 <conditional name="cm_opts">
246 <param name="cm_opts_selector" value="histdb"/> 230 <param name="cm_opts_selector" value="histdb"/>
247 <param name="cmfile" value="cmsearch_input1.cm"/> 231 <param name="cmfile" value="cmsearch_input1.cm"/>
248 </conditional> 232 </conditional>
249 <param name="seqdb" value="cmsearch_input2.fa"/> 233 <param name="seqdb" value="cmsearch_input2.fa"/>
250 <output name="outfile" file="cmsearch_result.tabular"/> 234 <output name="outfile" file="cmsearch_result.tabular"/>
251 </test> 235 </test>
236 <test expect_num_outputs="1">
237 <conditional name="cm_opts">
238 <param name="cm_opts_selector" value="db"/>
239 <param name="database" value="cmsearch_input1.cm"/>
240 </conditional>
241 <param name="seqdb" value="cmsearch_input2.fa"/>
242 <output name="outfile" file="cmsearch_result.tabular"/>
243 </test>
252 </tests> 244 </tests>
253 245
254 <help> 246 <help>
255 <![CDATA[ 247 <![CDATA[
256 248