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comparison cmalign.xml @ 20:b10f7688d14c draft

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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 10:26:56 +0000
parents 94cc7ef25867
children
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19:94cc7ef25867 20:b10f7688d14c
1 <tool id="infernal_cmalign" name="cmalign" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="infernal_cmalign" name="cmalign" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>Align sequences to a covariance model against a sequence database</description> 2 <description>Align sequences to a covariance model against a sequence database</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="xrefs"/>
6 <expand macro="requirements" /> 7 <expand macro="requirements" />
7 <expand macro="stdio" /> 8 <expand macro="stdio" />
8 <expand macro="xrefs"/>
9 <command> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 11
12 cmalign 12 cmalign
13 ## Infernal Options 13 ## Infernal Options
31 #end if 31 #end if
32 #if $speed_memory_cont.hmm_banding.banding_selector=="--nonbanded" 32 #if $speed_memory_cont.hmm_banding.banding_selector=="--nonbanded"
33 --mxsize $speed_memory_cont.hmm_banding.mxsize 33 --mxsize $speed_memory_cont.hmm_banding.mxsize
34 #end if 34 #end if
35 35
36 #if $other_opts.mapali_opt.mapali_cond 36 #if $other_opts.mapali_opt.mapali_cond=="true"
37 --mapali '$other_opts.mapali_opt.mapali' 37 --mapali '$other_opts.mapali_opt.mapali'
38 $other_opts.mapali_opt.mapstr 38 $other_opts.mapali_opt.mapstr
39 #end if 39 #end if
40 40
41 --informat $seqdb.ext 41 --informat $seqdb.ext
66 ]]> 66 ]]>
67 </command> 67 </command>
68 <inputs> 68 <inputs>
69 69
70 <param name="seqdb" type="data" format="fasta" label="Sequence database"/> 70 <param name="seqdb" type="data" format="fasta" label="Sequence database"/>
71 71 <expand macro="DB" />
72 <conditional name="cm_opts">
73 <param name="cm_opts_selector" type="select" label="Subject covariance models">
74 <option value="db" selected="True">Locally installed covariance models</option>
75 <option value="histdb">Covariance model from your history</option>
76 </param>
77 <when value="db">
78 <param name="database" type="select" label="Covariance models">
79 <options from_file="infernal.loc">
80 <column name="value" index="0"/>
81 <column name="name" index="1"/>
82 <column name="path" index="2"/>
83 </options>
84 </param>
85 </when>
86 <when value="histdb">
87 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
88 </when>
89 </conditional>
90
91 <param argument="-g" truevalue="-g" falsevalue="" checked="False" type="boolean" 72 <param argument="-g" truevalue="-g" falsevalue="" checked="False" type="boolean"
92 label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/> 73 label="Turn on the glocal alignment algorithm" help="... global with respect to the query model and local with respect to the target database."/>
93 74
94 <section name="alignment_algorithm_cont" title="Options controlling alignment algorithm" > 75 <section name="alignment_algorithm_cont" title="Options controlling alignment algorithm" >
95 <conditional name="alignment_algorithm"> 76 <conditional name="alignment_algorithm">
103 <when value="--sample"> 84 <when value="--sample">
104 <param argument="--seed" type="integer" value="0" label="set RNG seed to 'n'" help="if 0: one-time arbitrary seed"/> 85 <param argument="--seed" type="integer" value="0" label="set RNG seed to 'n'" help="if 0: one-time arbitrary seed"/>
105 </when> 86 </when>
106 </conditional> 87 </conditional>
107 <conditional name="notrunc_opt"> 88 <conditional name="notrunc_opt">
108 <param argument="--notrunc" truevalue="" falsevalue="--notrunc" checked="true" type="boolean" 89 <param argument="--notrunc" type="select"
109 label="Use truncated alignment algorithm" help=""/> 90 label="Use truncated alignment algorithm">
91 <option value="">Yes</option>
92 <option value="--notrunc">No</option>
93 </param>
110 <when value=""></when> 94 <when value=""></when>
111 <when value="--notrunc"> 95 <when value="--notrunc">
112 <param argument="--sub" type="boolean" truevalue="--sub" falsevalue="" checked="false" 96 <param argument="--sub" type="boolean" truevalue="--sub" falsevalue="" checked="false"
113 label="Build sub CM for columns b/t HMM predicted start/end points" help=""/> 97 label="Build sub CM for columns b/t HMM predicted start/end points" help=""/>
114 98
141 label="Use small memory divide and conquer algorithm" help="Allows CM alignment within practical memory limits, reducing the memory required for alignment. WARNING: It can only be used when --cyk,--noprob,--nonbanded,--notrunc are all enabled"/> 125 label="Use small memory divide and conquer algorithm" help="Allows CM alignment within practical memory limits, reducing the memory required for alignment. WARNING: It can only be used when --cyk,--noprob,--nonbanded,--notrunc are all enabled"/>
142 </section> 126 </section>
143 127
144 <section name="other_opts" title="Other options"> 128 <section name="other_opts" title="Other options">
145 <conditional name="mapali_opt"> 129 <conditional name="mapali_opt">
146 <param name="mapali_cond" type="boolean" checked="false" 130 <param name="mapali_cond" type="select"
147 label="Read the aligment file that used to build the CM" help="The alignment from the file is held fixed. This allows you to align sequences to a model with cmalign and view them in the context of an existing trusted multiple alignment."/> 131 label="Read the aligment file that used to build the CM" help="The alignment from the file is held fixed. This allows you to align sequences to a model with cmalign and view them in the context of an existing trusted multiple alignment.">
132 <option value="false">No</option>
133 <option value="true">Yes</option>
134 </param>
148 <when value="true"> 135 <when value="true">
149 <param argument="--mapali" type="data" format="fasta" 136 <param argument="--mapali" type="data" format="fasta"
150 label="The aligment file that used to build the CM" help=""/> 137 label="The aligment file that used to build the CM" help=""/>
151 <param argument="--mapstr" type="boolean" truevalue="--small" falsevalue="" checked="true" 138 <param argument="--mapstr" type="boolean" truevalue="--small" falsevalue="" checked="true"
152 label="Use small memory divide and conquer algorithm" help=""/> 139 label="Use small memory divide and conquer algorithm" help=""/>
179 <tests> 166 <tests>
180 <test> 167 <test>
181 <conditional name="cm_opts"> 168 <conditional name="cm_opts">
182 <param name="cm_opts_selector" value="histdb"/> 169 <param name="cm_opts_selector" value="histdb"/>
183 <param name="cmfile" value="cmalign_input2_tRNA5.c.cm"/> 170 <param name="cmfile" value="cmalign_input2_tRNA5.c.cm"/>
171 </conditional>
172 <param name="seqdb" value="cmalign_input_mrum_tRNAs10.fa"/>
173 <output name="outfile">
174 <assert_contents>
175 <has_text text="GGAGCUAUAGCUCAAU..GGC"/>
176 </assert_contents>
177 </output>
178 </test>
179 <test>
180 <conditional name="cm_opts">
181 <param name="cm_opts_selector" value="db"/>
182 <param name="database" value="cmalign_input2_tRNA5.c.cm"/>
184 </conditional> 183 </conditional>
185 <param name="seqdb" value="cmalign_input_mrum_tRNAs10.fa"/> 184 <param name="seqdb" value="cmalign_input_mrum_tRNAs10.fa"/>
186 <output name="outfile"> 185 <output name="outfile">
187 <assert_contents> 186 <assert_contents>
188 <has_text text="GGAGCUAUAGCUCAAU..GGC"/> 187 <has_text text="GGAGCUAUAGCUCAAU..GGC"/>