annotate chewbbaca.xml @ 0:a3b5bee8ae1b draft

Uploaded
author iss
date Fri, 03 May 2019 10:06:09 -0400
parents
children 872ed5ee7b98
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
1 <tool id="chewBBACA" name="chewBBACA" version="2.0">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
2 <description>BSR-Based Allele Calling Algorithm
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
3 </description>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
4 <requirements>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
5 <requirement type="package" version="3.6">Python</requirement>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
6 <requirement type="package" version="1.15.3">numpy</requirement>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
7 <requirement type="package" version="0.19.1">scipy</requirement>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
8 <requirement type="package" version="5.22.2.1">perl</requirement>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
9 <requirement type="package" version="1.72">biopython</requirement>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
10 <requirement type="package" version="3.8.1">plotly</requirement>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
11 <requirement type="package" version="1.8.2">SPARQLWrapper</requirement>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
12 <requirement type="package" version="0.23.4">pandas</requirement>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
13 <requirement type="package" version="2.5.0">blast</requirement>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
14 <requirement type="package" version="2.6.3">prodigal</requirement>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
15 <requirement type="package" version="2.1">clustalw</requirement>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
16 <requirement type="package" version="7.313">mafft</requirement>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
17 <requirement type="package" version="2.0.16">chewbbaca</requirement>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
18 </requirements>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
19 <!-- basic error handling -->
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
20 <stdio>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
21 <!-- Assume anything other than zero is an error -->
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
22 <exit_code range="1:" level="fatal" description="Tool exception" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
23 <exit_code range=":-1" level="fatal" description="Tool exception" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
24 </stdio>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
25 <command>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
26 perl
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
27 $__tool_directory__/chewBBACA.pl $selectFunction.myFunctions
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
28 #if str( $selectFunction.myFunctions ) in ('CreateSchema', 'AlleleCall')
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
29 '${",".join(map(str, $selectFunction.input1))}'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
30 #elif str( $selectFunction.myFunctions ) in ('SchemaEvaluator', 'TestGenomeQuality', 'ExtractCgMLST', 'RemoveGenes')
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
31 $selectFunction.input1
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
32 #else
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
33 'NULL'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
34 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
35 #if str( $selectFunction.myFunctions ) == 'AlleleCall'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
36 #set $input_names = []
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
37 #for $input in $selectFunction.input1
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
38 $input_names.append($input.element_identifier)
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
39 #end for
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
40 #set $input_name = ",".join(map(str, $input_names))
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
41 '$input_name'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
42 #else
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
43 'NULL'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
44 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
45 #if str( $selectFunction.myFunctions ) == 'CreateSchema'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
46 '$schema'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
47 #elif str( $selectFunction.myFunctions ) == 'AlleleCall'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
48 '$statistics,$contigsinfo,$alleles,$logginginfo,$repeatedloci'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
49 #elif str( $selectFunction.myFunctions ) == 'SchemaEvaluator'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
50 '$schemaplot'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
51 #elif str( $selectFunction.myFunctions ) == 'TestGenomeQuality'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
52 '$thresholdplot,$removedgenomes'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
53 #elif str( $selectFunction.myFunctions ) == 'RemoveGenes'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
54 '$removedgenes'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
55 #else
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
56 'NULL'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
57 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
58
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
59 "chewBBACA.py $selectFunction.myFunctions
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
60 #if str( $selectFunction.myFunctions ) in ('CreateSchema', 'AlleleCall', 'TestGenomeQuality', 'ExtractCgMLST')
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
61 -o output_dir
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
62 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
63 #if str( $selectFunction.myFunctions ) == 'RemoveGenes'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
64 -o output_removegenes
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
65 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
66 #if str( $selectFunction.myFunctions ) in ('CreateSchema', 'AlleleCall')
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
67 -i input_dir
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
68 --cpu \${GALAXY_SLOTS:-4}
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
69 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
70 #if str( $selectFunction.myFunctions ) in ('SchemaEvaluator', 'TestGenomeQuality', 'ExtractCgMLST', 'RemoveGenes')
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
71 -i $selectFunction.input1
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
72 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
73 #if str( $selectFunction.myFunctions ) in ('CreateSchema', 'AlleleCall')
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
74 #if $selectFunction.bsr
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
75 --bsr $selectFunction.bsr
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
76 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
77
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
78 #if $selectFunction.ptfmode.ptf_select=="system"
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
79 --ptf ${ filter( lambda x: str( x[0] ) == str( $selectFunction.ptfmode.ptf_system ), $__app__.tool_data_tables[ 'chewbbaca_ptfs' ].get_fields() )[0][-1] }
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
80 #elif $selectFunction.ptfmode.ptf_select=="user"
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
81 --ptf $selectFunction.ptfmode.ptf_user
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
82 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
83 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
84 #if str( $selectFunction.myFunctions ) == 'CreateSchema'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
85 #if $selectFunction.minBpLocus
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
86 -l $selectFunction.minBpLocus
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
87 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
88 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
89 #if str( $selectFunction.myFunctions ) == 'AlleleCall'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
90 #if $selectFunction.mode.schema_select=="system"
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
91 -g ${ filter( lambda x: str( x[0] ) == str( $selectFunction.mode.reference ), $__app__.tool_data_tables[ 'chewbbaca_schemas' ].get_fields() )[0][-1] }
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
92 #else
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
93 -g $selectFunction.mode.genes
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
94 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
95 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
96 #if str( $selectFunction.myFunctions ) == 'SchemaEvaluator'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
97 --cpu \${GALAXY_SLOTS:-4}
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
98 #if $selectFunction.conserved
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
99 -p
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
100 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
101 -l output_rms/SchemaEvaluator.html
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
102 -ta $selectFunction.ncbiTA
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
103 -t $selectFunction.threshold
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
104 #if $selectFunction.title
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
105 --title '$selectFunction.title'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
106 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
107 -s $selectFunction.numBoxplots
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
108 #if $selectFunction.light
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
109 --light
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
110 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
111 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
112 #if str( $selectFunction.myFunctions ) == 'TestGenomeQuality'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
113 -n $selectFunction.maxNumIterations
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
114 -t $selectFunction.maxThreshold
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
115 -s $selectFunction.stepThreshold
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
116 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
117 #if str( $selectFunction.myFunctions ) == 'ExtractCgMLST'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
118 #if $selectFunction.genes
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
119 -r $selectFunction.genes
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
120 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
121 #if $selectFunction.genomes
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
122 -g $selectFunction.genomes
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
123 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
124 #if $selectFunction.maxPresence
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
125 -p $selectFunction.maxPresence
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
126 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
127 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
128 #if str( $selectFunction.myFunctions ) == 'RemoveGenes'
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
129 -g $selectFunction.genes
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
130 #end if
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
131 "
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
132 </command>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
133
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
134 <inputs>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
135 <conditional name="selectFunction">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
136 <param name="myFunctions" type="select" label="Select function">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
137 <option value="CreateSchema">CreateSchema: Create a gene by gene schema based on genomes</option>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
138 <option value="AlleleCall" selected="true">AlleleCall: Perform allele call for target genomes</option>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
139 <option value="SchemaEvaluator">SchemaEvaluator: Tool that builds an html output to better navigate/visualize your schema</option>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
140 <option value="TestGenomeQuality">TestGenomeQuality: Analyze your allele call output to refine schemas</option>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
141 <option value="ExtractCgMLST">ExtractCgMLST: Select a subset of loci without missing data (to be used as PHYLOViZ input)</option>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
142 <option value="RemoveGenes">RemoveGenes: Remove a provided list of loci from your allele call output</option>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
143 </param>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
144 <when value="CreateSchema">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
145 <param name="input1" format="fasta" type="data" multiple="true" label="Selection of genome files (fasta)" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
146 <param name="bsr" type="text" value="0.6" optional="true" label="minimum BSR score" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
147 <conditional name="ptfmode">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
148 <param name="ptf_select" type="select" display="radio" label="Which Prodigal training file would you like to use?">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
149 <option value="system" selected="True">System training file</option>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
150 <option value="user">Own training file</option>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
151 </param>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
152 <when value="system">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
153 <param name="ptf_system" type="select" label="Choose Prodigal training file">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
154 <options from_data_table="chewbbaca_ptfs" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
155 </param>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
156 </when>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
157 <when value="user">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
158 <param name="ptf_user" format="binary" type="data" optional="true" multiple="false" label="Prodigal Training File" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
159 </when>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
160 </conditional>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
161 <param name="minBpLocus" type="integer" value="200" optional="true" label="minimum bp locus lenght" help="Integer" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
162 </when>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
163 <when value="AlleleCall">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
164 <param name="input1" format="fasta" type="data" multiple="true" label="Selection of genome files (fasta)" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
165 <conditional name="mode">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
166 <param name="schema_select" type="select" display="radio" label="Which schema would you like to use as a reference?">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
167 <option value="system" selected="True">System reference</option>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
168 <option value="user">Own reference</option>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
169 </param>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
170 <when value="system">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
171 <param name="reference" type="select" label="Choose reference">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
172 <options from_data_table="chewbbaca_schemas" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
173 </param>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
174 </when>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
175 <when value="user">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
176 <param name="genes" format="txt" type="data" label="File with list of genes (fasta)" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
177 </when>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
178 </conditional>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
179 <param name="bsr" type="text" value="0.6" optional="true" label="minimum BSR score" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
180 <conditional name="ptfmode">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
181 <param name="ptf_select" type="select" display="radio" label="Which Prodigal training file would you like to use?">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
182 <option value="system">System training file</option>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
183 <option value="user">Own training file</option>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
184 <option value="noptf" selected="True">No training file</option>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
185 </param>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
186 <when value="system">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
187 <param name="ptf_system" type="select" label="Choose Prodigal training file">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
188 <options from_data_table="chewbbaca_ptfs" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
189 </param>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
190 </when>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
191 <when value="user">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
192 <param name="ptf_user" format="binary" type="data" optional="true" multiple="false" label="Prodigal Training File" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
193 </when>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
194 <when value="noptf" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
195 </conditional>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
196 <!--<param name="forceContinue" type="boolean" truevalue="true" falsevalue="false" checked="False" label="force continue" />-->
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
197 <!--<param name="forceReset" type="boolean" truevalue="true" falsevalue="false" checked="False" label="force reset" />-->
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
198 <!--<param name="jsonFile" type="boolean" truevalue="true" falsevalue="false" checked="False" label="report in json file" />-->
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
199 </when>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
200 <when value="SchemaEvaluator">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
201 <param name="input1" format="txt" type="data" label="File with list of genes (fasta)" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
202 <param name="conserved" type="boolean" truevalue="true" falsevalue="false" checked="False" label="One bad allele still makes gene conserved" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
203 <param name="ncbiTA" type="integer" value="11" optional="true" label="ncbi translation table" help="Integer" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
204 <param name="threshold" type="float" value="0.05" optional="true" label="Threshold" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
205 <param name="title" type="text" value="My Analyzed wg/cg MLST Schema - Rate My Schema" optional="true" label="title on the html plot" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
206 <param name="numBoxplots" type="integer" value="500" optional="true" label="number of boxplots per page (more than 500 can make the page very slow)" help="Integer" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
207 <param name="light" type="boolean" truevalue="true" falsevalue="false" checked="False" label="skip clustal and mafft run" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
208 </when>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
209 <when value="TestGenomeQuality">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
210 <param name="input1" format="tsv" type="data" label="raw allele call matrix file" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
211 <param name="maxNumIterations" type="integer" value="12" label="maximum number of iterations" help="Each iteration removes a set of genomes over the defined threshold (-t) and recalculates all loci presence percentages" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
212 <param name="maxThreshold" type="integer" value="200" label="maximum threshold of bad calls above 95 percent" help="This threshold represents the maximum number of missing loci allowed, for each genome independently, before removing it (genome)" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
213 <param name="stepThreshold" type="integer" value="5" label="step between each threshold analysis (suggested 5)" help="Integer" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
214 </when>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
215 <when value="ExtractCgMLST">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
216 <param name="input1" format="tsv" type="data" label="input file to clean" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
217 <param name="genes" format="txt" type="data" optional="true" label="list of genes to remove, one per line" help="e.g. the list of gene detected by ParalogPrunning.py" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
218 <param name="genomes" format="txt" type="data" optional="true" label="list of genomes to remove, one per line" help="e.g. list of genomes to be removed selected based on testGenomeQuality results" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
219 <param name="maxPresence" type="float" value="1.0" optional="true" label="maximum presence (e.g 0.95)" >
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
220 <validator type="in_range" min="0" max="1" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
221 </param>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
222 </when>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
223 <when value="RemoveGenes">
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
224 <param name="input1" format="tsv" type="data" label="main matrix file from which to remove" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
225 <param name="genes" format="txt" type="data" label="list of genes to remove" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
226 </when>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
227 </conditional>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
228 </inputs>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
229
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
230 <!-- define outputs -->
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
231 <outputs>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
232 <data format="txt" name="schema" label="${tool.name}:CreateSchema on ${on_string}" >
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
233 <filter>selectFunction['myFunctions'] == "CreateSchema"</filter>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
234 </data>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
235 <data format="tsv" name="statistics" label="${tool.name}:AlleleCall on ${on_string}: Statistics" >
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
236 <filter>selectFunction['myFunctions'] == "AlleleCall"</filter>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
237 </data>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
238 <data format="tsv" name="contigsinfo" label="${tool.name}:AlleleCall on ${on_string}: Contigs Info" >
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
239 <filter>selectFunction['myFunctions'] == "AlleleCall"</filter>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
240 </data>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
241 <data format="tsv" name="alleles" label="${tool.name}:AlleleCall on ${on_string}: Alleles" >
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
242 <filter>selectFunction['myFunctions'] == "AlleleCall"</filter>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
243 </data>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
244 <data format="txt" name="logginginfo" label="${tool.name}:AlleleCall on ${on_string}: Logging info" >
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
245 <filter>selectFunction['myFunctions'] == "AlleleCall"</filter>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
246 </data>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
247 <data format="txt" name="repeatedloci" label="${tool.name}:AlleleCall on ${on_string}: Repeated Loci" >
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
248 <filter>selectFunction['myFunctions'] == "AlleleCall"</filter>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
249 </data>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
250 <data format="tar" name="schemaplot" label="${tool.name}:SchemaEvaluator on ${on_string}" >
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
251 <filter>selectFunction['myFunctions'] == "SchemaEvaluator"</filter>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
252 </data>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
253 <data format="html" name="thresholdplot" from_work_dir="output_dir/GenomeQualityPlot.html" label="${tool.name}:TestGenomeQuality on ${on_string}: Plot" >
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
254 <filter>selectFunction['myFunctions'] == "TestGenomeQuality"</filter>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
255 </data>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
256 <data format="tsv" name="removedgenomes" from_work_dir="output_dir/removedGenomes.txt" label="${tool.name}:TestGenomeQuality on ${on_string}: Removed genomes" >
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
257 <filter>selectFunction['myFunctions'] == "TestGenomeQuality"</filter>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
258 </data>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
259 <data format="tsv" name="cgmlst" from_work_dir="output_dir/cgMLST.tsv" label="${tool.name}:ExtractCgMLST on ${on_string}: cgMLST" >
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
260 <filter>selectFunction['myFunctions'] == "ExtractCgMLST"</filter>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
261 </data>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
262 <data format="txt" name="cgmlstschema" from_work_dir="output_dir/cgMLSTschema.txt" label="${tool.name}:ExtractCgMLST on ${on_string}: cgMLSTschema" >
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
263 <filter>selectFunction['myFunctions'] == "ExtractCgMLST"</filter>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
264 </data>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
265 <data format="tsv" name="removedgenes" from_work_dir="output_removegenes.tsv" label="${tool.name}:RemoveGenes on ${on_string}" >
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
266 <filter>selectFunction['myFunctions'] == "RemoveGenes"</filter>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
267 </data>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
268 </outputs>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
269 <tests>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
270 <test>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
271 <param name="selectFunction['myFunctions']" value="AlleleCall" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
272 <param name="input1" value="a_contigs.fasta" ftype="fasta" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
273 <param name="selectFunction.mode['schema_select']" value="system" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
274 <param name="selectFunction.mode['reference']" value="schema_pubMLST" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
275 <param name="selectFunction.mode['ptf_select']" value="noptf" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
276 <output name="statistics" >
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
277 <assert_contents>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
278 <has_text text="a_contigs.fasta" />
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
279 </assert_contents>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
280 </output>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
281 </test>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
282 </tests>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
283 <help>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
284 **chewBBACA** stands for "BSR-Based Allele Calling Algorithm". The "chew" part could be thought of as "Comprehensive and Highly Efficient Workflow"
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
285 but at this point still it needs a bit of work to make that claim so we just add "chew" to add extra coolness to the software name.
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
286 This tool is in beta test.
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
287
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
288 The development of the tools have been supported by INNUENDO project (https://www.innuendoweb.org) co-funded by the European Food Safety Authority (EFSA), grant agreement GP/EFSA/AFSCO/2015/01/CT2
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
289 ("New approaches in identifying and characterizing microbial and chemical hazards") and by the ONEIDA project (LISBOA-01-0145-FEDER-016417) co-funded by FEEI - “Fundos Europeus Estruturais e de Investimento”
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
290 from “Programa Operacional Regional Lisboa 2020” and by national funds from FCT - “Fundação para a Ciência e a Tecnologia” and BacGenTrack (TUBITAK/0004/2014)
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
291 [FCT/ Scientific and Technological Research Council of Turkey (Türkiye Bilimsel ve Teknolojik Araşrrma Kurumu, TÜBITAK)].
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
292 </help>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
293 <citations>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
294 <citation type="bibtex">@ARTICLE{andrews_s,
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
295 author = {Rossi, M and Silva, M and Ribeiro-Gonçalves, B and Silva, DN and Machado, MP and Oleastro, M and Borges, V and Isidro, J and Gomes, JP and Vieira, L and Barker, DOR and Llarena, AK and Halkilahti,
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
296 J and Jaakkonen, A and Palma, F and Culebro, A and Kivistö, R and Hänninen, ML and Laukkanen-Ninios, R and Fredriksson-Ahomaa, M and Salmenlinna, S and Hakkinen, M and Garaizer, J and Bikandi, J and Hilbert,
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
297 F and Taboada, EN and Carriço, JA},
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
298 keywords = {bioinformatics, ngs, mlst},
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
299 title = {{INNUENDO whole and core genome MLST databases and schemas for foodborne pathogens}},
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
300 url = {https://github.com/TheInnuendoProject/chewBBACA_schemas}
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
301 }</citation>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
302 <citation type="doi">10.1099/mgen.0.000166</citation>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
303 <citation type="doi">10.1371/journal.pgen.1007261</citation>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
304 </citations>
a3b5bee8ae1b Uploaded
iss
parents:
diff changeset
305 </tool>