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comparison hmmemit.xml @ 3:7b7ff4d209f7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
author iuc
date Sat, 07 Apr 2018 03:50:15 -0400
parents f48f9bbfcfd8
children 1cd4d0cf8fd9
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2:fee2f3f60f58 3:7b7ff4d209f7
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="hmmer_hmmemit" name="hmmemit" version="@WRAPPER_VERSION@.0"> 2 <tool id="hmmer_hmmemit" name="hmmemit" version="@TOOL_VERSION@">
3 <description>sample sequence(s) from a profile HMM</description> 3 <description>sample sequence(s) from a profile HMM</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
21 --minu $oformat.minu 21 --minu $oformat.minu
22 -C 22 -C
23 #else: 23 #else:
24 -N $oformat.N_smp 24 -N $oformat.N_smp
25 -p 25 -p
26 #if $oformat.L: 26 #if str($oformat.L):
27 -L $oformat.L 27 -L $oformat.L
28 #end if 28 #end if
29 $oformat.emission_profiles 29 $oformat.emission_profiles
30 #end if 30 #end if
31 31
32
33 @SEED@ 32 @SEED@
34 33
35 $hmmfile 34 '$hmmfile'
36 > $output 35 > '$output'
37 ]]></command> 36 ]]></command>
38 <inputs> 37 <inputs>
39 <expand macro="input_hmm" /> 38 <expand macro="input_hmm" />
40 39
41 <conditional name="oformat"> 40 <conditional name="oformat">
42 <param name="oformat_select" type="select" label="Output Format"> 41 <param name="oformat_select" type="select" label="Output Format">
45 <option value="mrcs">Majority-Rule Concensus Sequence</option> 44 <option value="mrcs">Majority-Rule Concensus Sequence</option>
46 <option value="mrcsf">Fancier Concensus Sequence</option> 45 <option value="mrcsf">Fancier Concensus Sequence</option>
47 <option value="sample">Sample sequences from profile, not core model</option> 46 <option value="sample">Sample sequences from profile, not core model</option>
48 </param> 47 </param>
49 <when value="fasta"> 48 <when value="fasta">
50 <param name="N_fa" type="integer" value="1" min="1" help="(-N)" 49 <param name="N_fa" argument="-N" type="integer" min="1" value="1"
51 label="Number of sequences to generate"/> 50 label="Number of sequences to generate"/>
52 </when> 51 </when>
53 <when value="aln"> 52 <when value="aln">
54 <param name="N_aln" type="integer" value="1" min="1" help="(-N)" 53 <param name="N_aln" argument="-N" type="integer" min="1" value="1"
55 label="Number of sequences to generate"/> 54 label="Number of sequences to generate"/>
56 </when> 55 </when>
57 <when value="mrcs"> 56 <when value="mrcs" />
58 </when>
59 <when value="mrcsf"> 57 <when value="mrcsf">
60 <param name="minl" type="float" value="0.7" help="(--minl)" 58 <param argument="--minl" type="float" value="0.7"
61 label="show consensus as 'any' (X/N) unless >= this fraction"/> 59 label="show consensus as 'any' (X/N) unless >= this fraction"/>
62 <param name="minu" type="float" value="0.2" help="(--minu)" 60 <param argument="--minu" type="float" value="0.2"
63 label="show consensus as upper case if >= this fraction"/> 61 label="show consensus as upper case if >= this fraction"/>
64 </when> 62 </when>
65 <when value="sample"> 63 <when value="sample">
66 <param name="N_smp" type="integer" value="1" min="1" help="(-N)" 64 <param name="N_smp" argument="-N" type="integer" min="1" value="1"
67 label="Number of sequences to generate"/> 65 label="Number of sequences to generate"/>
68 <param name="L" type="integer" optional="True" help="(-L)" 66 <param argument="-L" type="integer" optional="true"
69 label="Expected length of profile"/> 67 label="Expected length of profile"/>
70 68
71 <param name="emission_profiles" type="select" label="Emission profile options"> 69 <param name="emission_profiles" type="select" label="Emission profile options">
72 <option value="--local" selected="true">configure profile in multihit local mode</option> 70 <option value="--local" selected="true">configure profile in multihit local mode</option>
73 <option value="--unilocal">configure profile in unilocal mode</option> 71 <option value="--unilocal">configure profile in unilocal mode</option>
79 77
80 78
81 <expand macro="seed"/> 79 <expand macro="seed"/>
82 </inputs> 80 </inputs>
83 <outputs> 81 <outputs>
84 <data format="fasta" name="output" label="Sequences generated from $hmmfile.name"> 82 <data name="output" format="fasta" label="Sequences generated from $hmmfile.name">
85 <change_format> 83 <change_format>
86 <when input="oformat_select" value="aln" format="stockholm"/> 84 <when input="oformat_select" value="aln" format="stockholm"/>
87 <!-- the rest are fasta --> 85 <!-- the rest are fasta -->
88 </change_format> 86 </change_format>
89 </data> 87 </data>
168 clude nonhomologous as well as homologous sequences, and may contain more than 166 clude nonhomologous as well as homologous sequences, and may contain more than
169 one homologous sequence segment. By default, the profile is in multihit local 167 one homologous sequence segment. By default, the profile is in multihit local
170 mode, and the target sequence length is configured for L=400. 168 mode, and the target sequence length is configured for L=400.
171 169
172 @ATTRIBUTION@ 170 @ATTRIBUTION@
173 ]]></help> 171 ]]></help>
174 <expand macro="citation"/> 172 <expand macro="citation"/>
175 </tool> 173 </tool>