Mercurial > repos > iuc > hmmer_hmmemit
comparison hmmemit.xml @ 3:7b7ff4d209f7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
author | iuc |
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date | Sat, 07 Apr 2018 03:50:15 -0400 |
parents | f48f9bbfcfd8 |
children | 1cd4d0cf8fd9 |
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2:fee2f3f60f58 | 3:7b7ff4d209f7 |
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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> |