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1 <tool id="infernal_cmstat" name="Summary statistics" version="1.1.0.1">
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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="1.1">infernal</requirement>
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6 <requirement type="package" version="8.22">gnu_coreutils</requirement>
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7 </requirements>
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8 <command>
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9 <![CDATA[
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10 ## a temp file is needed, because the standard tabular output from infernal is not usefull in Galaxy
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11 ## it will be converted to a tab delimited file and piped to Galaxy
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12 temp_tabular_output=\$(mktemp);
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13
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14 cmstat
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15
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16 #if str($cm_opts.cm_opts_selector) == "db":
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17 $cm_opts.database.fields.path
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18 #else:
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19 $cm_opts.cmfile
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20 #end if
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21
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22 > \$temp_tabular_output
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23 ;
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24
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25 ## 1. replace all lines starting # (comment lines)
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26 ## 2. replace the first 18 spaces with tabs, 18th field is a free text field (can contain spaces)
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27 sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' \$temp_tabular_output > $outfile
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28
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29 ]]>
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30 </command>
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31 <inputs>
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32 <conditional name="cm_opts">
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33 <param name="cm_opts_selector" type="select" label="Subject covariance models">
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34 <option value="db" selected="True">Locally installed covariance models</option>
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35 <option value="histdb">Covariance model from your history</option>
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36 </param>
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37 <when value="db">
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38 <param name="database" type="select" label="Covariance models">
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39 <options from_file="infernal.loc">
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40 <column name="value" index="0"/>
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41 <column name="name" index="1"/>
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42 <column name="path" index="2"/>
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43 </options>
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44 </param>
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45 </when>
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46 <when value="histdb">
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47 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
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48 </when>
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49 </conditional>
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50 </inputs>
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51 <outputs>
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52 <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
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53 </outputs>
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54 <help>
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55 <![CDATA[
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56
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57
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58 **What it does**
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59
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60 The cmstat utility prints out a tabular file of summary statistics for each given covariance model.
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61
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62
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63 Output format
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64 -------------
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65
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66 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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67 tabular format.
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68
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69 The columns are:
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70
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71 (1) The index of this profile, numbering each on in the file starting from 1.
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72 (2) The name of the profile.
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73 (3) The optional accession of the profile, or ”-” if there is none.
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74 (4) The number of sequences that the profile was estimated from.
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75 (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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76 (6) The length of the model in consensus residues (match states).
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77 (7) The expected maximum length of a hit to the model.
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78 (8) The number of basepairs in the model.
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79 (9) The number of bifurcations in the model.
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80 (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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81 (11) Mean relative entropy per match state, in bits. This is the expected (mean) score per con-
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82 sensus position. This is what the default entropy-weighting method for effective sequence
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83 number estimation focuses on, so for default Infernal, this value will often reflect the default
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84 target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”.
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85 (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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86 relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs.
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87
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88
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89 For further questions please refere to the Infernal Userguide_.
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90
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91 .. _Userguide: http://selab.janelia.org/software/infernal/Userguide.pdf
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92
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93
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94 How do I cite Infernal?
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95 -----------------------
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96
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97 The recommended citation for using Infernal 1.1 is E. P. Nawrocki and S. R. Eddy, Infernal 1.1: 100-fold faster RNA homology searches , Bioinformatics 29:2933-2935 (2013).
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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 ]]>
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104 </help>
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105 </tool>
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