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1 <tool id="infernal_cmstat" name="Summary statistics" version="1.1.0.0">
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2 <description>for covariance model (cmstat)</description>
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3 <requirements>
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4 <requirement type="package">infernal</requirement>
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5 <requirement type="package" version="1.1rc4">infernal</requirement>
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6 <requirement type="package" version="8.21">gnu_coreutils</requirement>
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7 </requirements>
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8 <command>
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9 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
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10 ## it will be converted to a tab delimited file and piped to Galaxy
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11 temp_tabular_output=\$(mktemp);
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12
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13 cmstat
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14
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15 #if $cm_opts.cm_opts_selector == "db":
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16 $cm_opts.database.fields.path
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17 #else:
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18 $cm_opts.cmfile
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19 #end if
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20
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21 > \$temp_tabular_output
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22 ;
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23
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24 ## 1. replace all lines starting # (comment lines)
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25 ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces)
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26 sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile
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27
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28 </command>
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29 <inputs>
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30 <conditional name="cm_opts">
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31 <param name="cm_opts_selector" type="select" label="Subject covariance models">
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32 <option value="db" selected="True">Locally installed covariance models</option>
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33 <option value="histdb">Covariance model from your history</option>
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34 </param>
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35 <when value="db">
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36 <param name="database" type="select" label="Covariance models">
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37 <options from_file="infernal.loc">
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38 <column name="value" index="0"/>
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39 <column name="name" index="1"/>
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40 <column name="path" index="2"/>
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41 </options>
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42 </param>
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43 </when>
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44 <when value="histdb">
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45 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
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46 </when>
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47 </conditional>
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48 </inputs>
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49 <outputs>
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50 <data format="tabular" name="outfile" label="cmsearch on ${on_string}"/>
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51 </outputs>
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52 <help>
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53
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54
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55 **What it does**
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56
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57 The cmstat utility prints out a tabular file of summary statistics for each given covariance model.
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58
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59
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60 Output format
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61 -------------
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62
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63 By default, cmstat prints general statistics of the model and the alignment it was built from, one line per model in a
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64 tabular format.
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65
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66 The columns are:
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67
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68 (1) The index of this profile, numbering each on in the file starting from 1.
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69 (2) The name of the profile.
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70 (3) The optional accession of the profile, or ”-” if there is none.
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71 (4) The number of sequences that the profile was estimated from.
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72 (5) The effective number of sequences that the profile was estimated from, after Infernal applied an effective sequence number calculation such as the default entropy weighting.
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73 (6) The length of the model in consensus residues (match states).
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74 (7) The expected maximum length of a hit to the model.
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75 (8) The number of basepairs in the model.
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76 (9) The number of bifurcations in the model.
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77 (10) What type of model will be used by default in cmsearch and cmscan for this profile, either ”cm” or ”hmm”. For profiles with 0 basepairs, this will be ”hmm” (unless the --nohmmonly option is used). For all other profiles, this will be ”cm”.
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78 (11) Mean relative entropy per match state, in bits. This is the expected (mean) score per con-
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79 sensus position. This is what the default entropy-weighting method for effective sequence
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80 number estimation focuses on, so for default Infernal, this value will often reflect the default
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81 target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”.
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82 (12) Mean relative entropy per match state, in bits, if the CM were transformed into an HMM (information from structure is ignored). The larger the difference between the CM and HMM
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83 relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs.
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84
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85
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86 For further questions please refere to the Infernal Userguide_.
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87
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88 .. _Userguide: http://selab.janelia.org/software/infernal/Userguide.pdf
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89
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90
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91 How do I cite Infernal?
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92 -----------------------
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93
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94 The Infernal 1.0 paper (Nawrocki et al., 2009) is the best paper to reference.
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95 If you’re writing for an enlightened (url-friendly) journal, you may want to cite the webpage
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96 http://infernal.janelia.org/ because it is kept up-to-date. We hope to publish a paper related to
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97 Infernal version 1.1 soon.
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98
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99 **Galaxy Wrapper Author**::
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100
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101 * Bjoern Gruening, University of Freiburg
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102
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103 </help>
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104 </tool>
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