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planemo upload commit bdb474693831a3375db79755e88641ad32b3b4e6-dirty
author galaxyp
date Sun, 21 Feb 2016 11:20:31 -0500
parents b6b2ac0716eb
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1 <tool id="decoyfasta" name="Create Decoy Database (reverse)" version="0.1.0"> 1 <tool id="decoyfasta" name="Create Decoy Database (reverse)" version="0.2.0">
2 <description>Creates a decoy search database by adding reverse 2 <description>Creates a decoy search database by adding reverse
3 sequences to an existing database.</description> 3 sequences to an existing database</description>
4 4 <requirements>
5 <requirements> 5 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
6 <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> 6 </requirements>
7 </requirements> 7 <command>
8 8 <![CDATA[
9 <command> 9 decoyFASTA
10 decoyFASTA ${input} ${output} ${include_original} 10 ${input}
11 #if $freq_type.advanced == "yes" 11 ${output}
12 -t${frequency} ${tag} 12 ${include_original}
13 #for $extra_tag in $extra_tags 13 #if $freq_type.advanced == "yes"
14 -t${extra_tag.frequency} ${extra_tag.tag} 14 -t${frequency} ${tag}
15 #end for 15 #for $extra_tag in $extra_tags
16 #else 16 -t${extra_tag.frequency} ${extra_tag.tag}
17 -t1 ${freq_type.tag} 17 #end for
18 #end if 18 #else
19 </command> 19 -t1 ${freq_type.tag}
20 20 #end if
21 <inputs> 21 ]]>
22 <param format="fasta" name="input" type="data" label="FASTA Input" help="select input database from history in FASTA format" /> 22 </command>
23 <param name="include_original" type="boolean" truevalue="" falsevalue="-no_orig" label="Include original entries in output database" checked="True" help="(default) keep checked in all standard searches" /> 23 <inputs>
24 <conditional name="freq_type"> 24 <param format="fasta" name="input" type="data" label="FASTA Input" help="select input database from history in FASTA format" />
25 <param name="advanced" type="select" label="Specify advanced decoy frequency options?" help="&quot;Decoy Prefix&quot; will name the prefix of each decoy sequence, &quot;Frequency&quot; will specify how many decoy sequences are created"> 25 <param name="include_original" type="boolean" truevalue="" falsevalue="-no_orig" label="Include original entries in output database" checked="True" help="(default) keep checked in all standard searches" />
26 <option value="no">No, just create database with one reversed sequence for every input sequence</option> 26 <conditional name="freq_type">
27 <option value="yes">Yes, I want to specify multiple prefixes and specific frequencies</option> 27 <param name="advanced" type="select" label="Specify advanced decoy frequency options?" help="&quot;Decoy Prefix&quot; will name the prefix of each decoy sequence, &quot;Frequency&quot; will specify how many decoy sequences are created">
28 </param> 28 <option value="no">No, just create database with one reversed sequence for every input sequence</option>
29 <when value="no"> 29 <option value="yes">Yes, I want to specify multiple prefixes and specific frequencies</option>
30 <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/> 30 </param>
31 </when> 31 <when value="no">
32 <when value="yes"> 32 <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/>
33 <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/> 33 </when>
34 <param name="frequency" type="integer" value="1" label="Decoy Frequency" /> 34 <when value="yes">
35 <repeat name="extra_tags" title="Additional Decoy Tags"> 35 <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/>
36 <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/> 36 <param name="frequency" type="integer" value="1" label="Decoy Frequency" />
37 <param name="frequency" type="integer" value="1" label="Decoy Frequency" /> 37 <repeat name="extra_tags" title="Additional Decoy Tags">
38 </repeat> 38 <param name="tag" type="text" value="decoy_" label="Decoy Prefix"/>
39 </when> 39 <param name="frequency" type="integer" value="1" label="Decoy Frequency" />
40 </conditional> 40 </repeat>
41 </inputs> 41 </when>
42 42 </conditional>
43 <outputs> 43 </inputs>
44 <data format="fasta" name="output" /> 44 <outputs>
45 </outputs> 45 <data format="fasta" name="output" />
46 46 </outputs>
47 <help> 47 <help>
48 <![CDATA[
48 **What it does** 49 **What it does**
49 50
50 Given an input database, this tool will produce another database with 51 Given an input database, this tool will produce another database with
51 reversed sequences to use as decoys for False Discovery Rate (FDR) estimation in protein search identification. This tool employs the decoyFASTA program from 52 reversed sequences to use as decoys for False Discovery Rate (FDR) estimation in protein search identification. This tool employs the decoyFASTA program from
52 the Transproteomic Pipeline. 53 the Transproteomic Pipeline.
53 54
54 ------ 55 ------
55 56
56 **Citation** 57 **Citation**
57 58
58 For the underlying tool, please cite `Proteomics. 2010 Mar;10(6):1150-9. A guided tour of the Trans-Proteomic Pipeline. Deutsch EW, Mendoza L, Shteynberg D, Farrah T, Lam H, Tasman N, Sun Z, Nilsson E, Pratt B, Prazen B, Eng JK, Martin DB, Nesvizhskii AI, Aebersold R. PMID 20101611` 59 If you use this tool in Galaxy, please cite Chilton J, et al. https://github.com/galaxyproteomics/
59 60 ]]>
60 If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/decoyfasta 61 </help>
61 </help> 62 <citations>
63 <citation type="doi">10.1002/pmic.200900375</citation>
64 </citations>
62 </tool> 65 </tool>