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comparison micomplete.xml @ 0:23e768cddc7d draft

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Initial commit of micomplete
author lionelguy
date Thu, 17 Oct 2013 08:39:52 -0400
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1 <tool id="micomplete" name="micomplete" version="0.1">
2 <description>Using hmm profiles of conserved proteins, reports how much complete a (single-cell amplified) genome is</description>
3 <requirements>
4 <requirement type="package" version="3.1b1">hmmer</requirement>
5 </requirements>
6 <command interpreter="perl">micomplete.pl
7 #if $hmm_source.hmm_source_type == "cached"
8 --hmm "${ hmm_source.profiles.fields.hmms }"
9 --weights "${ hmm_source.profiles.fields.weights }"
10 #else
11 --hmm "${ hmm_source.own_profiles }"
12 #if $hmm_source.weights.use_weights
13 --weights "${ hmm_source.weights.own_weights }"
14 #end if
15 #end if
16 --proteome $proteome
17 --cut-off $cutoff
18 #if $evalue
19 --evalue
20 #end if
21 #if $save_hmm_tab
22 --save-hmm-tab $hmm_tab
23 #end if
24 #if $save_hmm_alignments
25 --save-hmm-alignments $hmm_alignments
26 #end if
27 #if $save_res_tab
28 --save-result-tab $res_tab
29 #end if
30 --threads $threads > $output
31 </command>
32 <inputs>
33 <param name="proteome" type="data" format="fasta" label="Proteome file" />
34 <conditional name="hmm_source">
35 <param name="hmm_source_type" type="select" label="HMM file from history or from built-in profile?">
36 <option value="cached">Use a built-in profile</option>
37 <option value="history">Use a profile from the history</option>
38 </param>
39 <when value="cached">
40 <param name="profiles" type="select" label="Select a reference set">
41 <options from_data_table="micomplete_hmms">
42 <filter type="sort_by" column="2" />
43 </options>
44 </param>
45 </when>
46 <when value="history">
47 <param name="own_profiles" type="data" format="text" label="Select a HMM set in the history" />
48 <conditional name="weights">
49 <param name="use_weights" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Use weights?" />
50 <when value="True">
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"/>
52 </when>
53 </conditional>
54 </when>
55 </conditional>
56 <param name="cutoff" type="float" value="1e-10" label="E-value cutoff to include hits" />
57 <param name="evalue" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Show E-values on the output instead of 0/1?" />
58 <param name="save_res_tab" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Save per marker result tabular file?" />
59 <param name="save_hmm_tab" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Save HMM tab result file?" />
60 <param name="save_hmm_alignments" type="boolean" checked="false" truevalue="True" falsevalue="False" label="Save HMM alignments result file?" />
61 <param name="threads" type="integer" value="15" min="1" label="Number of threads to use" />
62 </inputs>
63 <outputs>
64 <data format="txt" name="output" label="Completeness report" />
65 <data format="tabular" name="res_tab" label="HMM report, tabular format">
66 <filter>save_res_tab is True</filter>
67 </data>
68 <data format="tabular" name="hmm_tab" label="HMM report, tabular format">
69 <filter>save_hmm_tab is True</filter>
70 </data>
71 <data format="txt" name="hmm_alignments" label="HMM alignments">
72 <filter>save_hmm_alignments is True</filter>
73 </data>
74 </outputs>
75 <help>
76 ***What it does***
77
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
79
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.
81
82 **License**
83
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.
85
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.
87
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/.
89 </help>
90 </tool>