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1 <tool id="micomplete" name="micomplete" version="0.1">
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2 <description>Using hmm profiles of conserved proteins, reports how much complete a (single-cell amplified) genome is</description>
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3 <requirements>
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4 <requirement type="package" version="3.1b1">hmmer</requirement>
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5 </requirements>
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6 <command interpreter="perl">micomplete.pl
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7 #if $hmm_source.hmm_source_type == "cached"
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8 --hmm "${ hmm_source.profiles.fields.hmms }"
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9 --weights "${ hmm_source.profiles.fields.weights }"
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10 #else
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11 --hmm "${ hmm_source.own_profiles }"
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12 #if $hmm_source.weights.use_weights
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13 --weights "${ hmm_source.weights.own_weights }"
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14 #end if
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15 #end if
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16 --proteome $proteome
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17 --cut-off $cutoff
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18 #if $evalue
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19 --evalue
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20 #end if
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21 #if $save_hmm_tab
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22 --save-hmm-tab $hmm_tab
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23 #end if
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24 #if $save_hmm_alignments
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25 --save-hmm-alignments $hmm_alignments
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26 #end if
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27 #if $save_res_tab
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28 --save-result-tab $res_tab
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29 #end if
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30 --threads $threads > $output
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31 </command>
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32 <inputs>
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33 <param name="proteome" type="data" format="fasta" label="Proteome file" />
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34 <conditional name="hmm_source">
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35 <param name="hmm_source_type" type="select" label="HMM file from history or from built-in profile?">
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36 <option value="cached">Use a built-in profile</option>
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37 <option value="history">Use a profile from the history</option>
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38 </param>
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39 <when value="cached">
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40 <param name="profiles" type="select" label="Select a reference set">
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41 <options from_data_table="micomplete_hmms">
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42 <filter type="sort_by" column="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="history">
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47 <param name="own_profiles" type="data" format="text" label="Select a HMM set in the history" />
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48 <conditional name="weights">
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49 <param name="use_weights" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Use weights?" />
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50 <when value="True">
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51 <param name="own_weights" type="data" format="tabular" label="Select a weight file (optional)" help="There should be exactly one weight for each profile in the profiles file"/>
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52 </when>
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53 </conditional>
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54 </when>
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55 </conditional>
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56 <param name="cutoff" type="float" value="1e-10" label="E-value cutoff to include hits" />
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57 <param name="evalue" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Show E-values on the output instead of 0/1?" />
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58 <param name="save_res_tab" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Save per marker result tabular file?" />
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59 <param name="save_hmm_tab" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Save HMM tab result file?" />
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60 <param name="save_hmm_alignments" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Save HMM alignments result file?" />
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61 <param name="threads" type="integer" value="15" min="1" label="Number of threads to use" />
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62 </inputs>
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63 <outputs>
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64 <data format="txt" name="output" label="Completeness report" />
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65 <data format="tabular" name="res_tab" label="HMM report, tabular format">
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66 <filter>save_res_tab is True</filter>
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67 </data>
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68 <data format="tabular" name="hmm_tab" label="HMM report, tabular format">
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69 <filter>save_hmm_tab is True</filter>
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70 </data>
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71 <data format="txt" name="hmm_alignments" label="HMM alignments">
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72 <filter>save_hmm_alignments is True</filter>
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73 </data>
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74 </outputs>
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75 <help>
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76 ***What it does***
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77
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78 Micomplete estimates the level of completion of a genome. This is particularly useful for single-cell amplified genomes. It aligns a proteome to a set of "markers" or conserved proteins, represented by a collection of HMM profiles, possibly with weights. It uses hmmsearch (http://hmmer.janelia.org/, see for example S.R Eddy, PLOS Comp Biol 2011, 7:e1002195) to align proteins
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79
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80 Weights are used to alleviate the effect of having/not having a specific contig which would contain many markers that are generally clustering together. Typically, ribosomal proteins, often used are markers, are often organized in operons. Thus, the impact of having/not having these operons is very important, and should be downplayed to get a more correct estimate.
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81
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82 **License**
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83
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84 This wrapper is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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85
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86 This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
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87
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88 You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
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89 </help>
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90 </tool> |
