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annotate cmstat.xml @ 6:ee4be6eadd34 draft

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author bgruening
date Fri, 10 Nov 2017 13:04:44 -0500
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children c9e29ac5d099
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1 <tool id="infernal_cmstat" name="cmstat" version="@VERSION@.0">
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2 <description>Summary statistics for covariance model </description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio" />
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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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14 cmstat
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15 #if str($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 > $outfile
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24 ]]>
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25 </command>
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26 <inputs>
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27 <conditional name="cm_opts">
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28 <param name="cm_opts_selector" type="select" label="Subject covariance models">
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29 <option value="db" selected="True">Locally installed covariance models</option>
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30 <option value="histdb">Covariance model from your history</option>
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31 </param>
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32 <when value="db">
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33 <param name="database" type="select" label="Covariance models">
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34 <options from_file="infernal.loc">
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35 <column name="value" index="0"/>
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36 <column name="name" index="1"/>
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37 <column name="path" index="2"/>
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38 </options>
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39 </param>
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40 </when>
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41 <when value="histdb">
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42 <param name="cmfile" type="data" format="cm" label="Covariance models file from the history."/>
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43 </when>
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44 </conditional>
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45 </inputs>
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46 <outputs>
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47 <data format="tabular" name="outfile" label="cmstat on ${on_string}"/>
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48 </outputs>
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49 <tests>
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50 <test>
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51 <conditional name="cm_opts">
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52 <param name="cm_opts_selector" value="histdb"/>
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53 <param name="cmfile" value="cmstat_input.cm"/>
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54 </conditional>
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55 <output name="outfile" >
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56 <assert_contents>
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57 <has_text text="idx"/>
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58 <has_text text="accession"/>
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59 <has_text text="nseq"/>
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60 </assert_contents>
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61 </output>
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62 </test>
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63 </tests>
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64 <help>
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65 <![CDATA[
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66
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68 **What it does**
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69
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70 The cmstat utility prints out a tabular file of summary statistics for each given covariance model.
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72
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73 **Output format**
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76 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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77 tabular format.
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79 The columns are:
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81 (1) The index of this profile, numbering each on in the file starting from 1.
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82 (2) The name of the profile.
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83 (3) The optional accession of the profile, or ”-” if there is none.
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84 (4) The number of sequences that the profile was estimated from.
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85 (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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86 (6) The length of the model in consensus residues (match states).
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87 (7) The expected maximum length of a hit to the model.
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88 (8) The number of basepairs in the model.
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89 (9) The number of bifurcations in the model.
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90 (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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91 (11) Mean relative entropy per match state, in bits. This is the expected (mean) score per con-
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92 sensus position. This is what the default entropy-weighting method for effective sequence
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93 number estimation focuses on, so for default Infernal, this value will often reflect the default
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94 target for entropy-weighting. If the ”model” field for this profile is ”hmm”, this field will be ”-”.
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95 (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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96 relative entropy, the more the model will rely on structural conservation relative sequence conservation when identifying homologs.
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97
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98
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99 For further questions please refere to the Infernal `Userguide <http://eddylab.org/infernal/Userguide.pdf>`_.
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100
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101 ]]>
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102 </help>
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103 <expand macro="citations" />
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104
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105 </tool>