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comparison blat_wrapper.xml @ 2:6265acc179ff draft

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Uploaded
author crs4
date Mon, 04 Nov 2013 06:35:53 -0500
parents c4ad58c4bc7d
children d78b8fe7ca83
comparison
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1:c4ad58c4bc7d 2:6265acc179ff
1 <tool id="blat_wrapper" name="BLAT" version="0.2"> 1 <tool id="blat_wrapper" name="BLAT" version="0.3">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="35">blat</requirement> 4 <requirement type="package" version="35">blat</requirement>
5 </requirements> 5 </requirements>
6 <version_command>blat|head -n 1</version_command> 6 <version_command>blat|head -n 1</version_command>
7 <command> 7 <command>
8 blat $database $query -t=$databaseType.databaseType_select -q=$databaseType.queryType 8 blat
9 #if $database_source.database_source_select == 'fasta_db'
10 $database_source.database.fields.path
11 #else if $database_source.database_source_select == 'twobit_db'
12 #if $database_source.range
13 $database_source.database.fields.path:$database_source.range
14 #else
15 $database_source.database.fields.path
16 #end if
17 #else
18 $database_source.database
19 #end if
20 $query -t=$databaseType.databaseType_select -q=$databaseType.queryType
9 #if str($databaseType.tileSize) 21 #if str($databaseType.tileSize)
10 -tileSize=$databaseType.tileSize 22 -tileSize=$databaseType.tileSize
11 #end if 23 #end if
12 #if str($stepSize) 24 #if str($stepSize)
13 -stepSize=$stepSize 25 -stepSize=$stepSize
65 -out=$out 77 -out=$out
66 $output > $logfile 78 $output > $logfile
67 </command> 79 </command>
68 80
69 <inputs> 81 <inputs>
70 <param name="database" type="data" format="fasta,twobit" label="Database" help="FASTA or 2bit format" /> 82 <conditional name="database_source">
71 <param name="query" type="data" format="fasta,twobit" label="Query" help="FASTA or 2bit format" /> 83 <param name="database_source_select" type="select" label="Database source">
72 84 <option value="fasta_db">Locally installed FASTA database</option>
85 <option value="twobit_db">Locally installed 2bit database</option>
86 <option value="file">FASTA or 2bit file from your history</option>
87 </param>
88 <when value="fasta_db">
89 <param name="database" type="select" label="Select a FASTA database">
90 <options from_data_table="all_fasta">
91 <filter type="sort_by" column="name" />
92 <validator type="no_options" message="No FASTA database available" />
93 </options>
94 </param>
95 </when>
96 <when value="twobit_db">
97 <param name="database" type="select" label="Select a 2bit database">
98 <options from_data_table="lastz_seqs">
99 <filter type="sort_by" column="name" />
100 <validator type="no_options" message="No 2bit database available" />
101 </options>
102 </param>
103 <param name="range" type="text" optional="true" value="" label="Restrict the search space to this genomic range in the sequence database" help="Format = 'chr1:250000-260000' (i.e. name:startposition-endposition)">
104 <validator type="regex" message="Invalid range">\w+:\d+-\d+</validator>
105 </param>
106 </when>
107 <when value="file">
108 <param name="database" type="data" format="fasta,twobit" label="Database file" help="FASTA or 2bit format" />
109 </when>
110 </conditional>
73 <conditional name="databaseType"> 111 <conditional name="databaseType">
74 <param name="databaseType_select" type="select" label="Database type (-t)"> 112 <param name="databaseType_select" type="select" label="Database type (-t)">
75 <option value="dna" selected="true">DNA sequence (dna)</option> 113 <option value="dna" selected="true">DNA sequence (dna)</option>
76 <option value="prot">Protein sequence (prot)</option> 114 <option value="prot">Protein sequence (prot)</option>
77 <option value="dnax">DNA sequence translated in six frames to protein (dnax)</option> 115 <option value="dnax">DNA sequence translated in six frames to protein (dnax)</option>
108 <validator type="in_range" min="1" /> 146 <validator type="in_range" min="1" />
109 </param> 147 </param>
110 <param name="minIdentity" type="integer" value="25" optional="true" label="Minimum sequence identity (%) (-minIdentity)" /> 148 <param name="minIdentity" type="integer" value="25" optional="true" label="Minimum sequence identity (%) (-minIdentity)" />
111 </when> 149 </when>
112 </conditional> 150 </conditional>
113 151 <param name="query" type="data" format="fasta,twobit" label="Query" help="FASTA or 2bit format" />
114 <!-- <param name="ooc" type="data" format="ooc" optional="true" label="Over-occuring N-mers file (-ooc) produced with blat -makeOoc" help="Use N as tileSize below." /> This should wait for a makeOoc wrapper --> 152 <!-- <param name="ooc" type="data" format="ooc" optional="true" label="Over-occuring N-mers file (-ooc) produced with blat -makeOoc" help="Use N as tileSize below." /> This should wait for a makeOoc wrapper -->
115 153
116 <param name="stepSize" type="integer" value="" optional="true" label="Spacing between tiles (-stepSize)" help="Default is tileSize"> 154 <param name="stepSize" type="integer" value="" optional="true" label="Spacing between tiles (-stepSize)" help="Default is tileSize">
117 <validator type="in_range" min="1" /> 155 <validator type="in_range" min="1" />
118 </param> 156 </param>
196 </change_format> 234 </change_format>
197 </data> 235 </data>
198 </outputs> 236 </outputs>
199 <tests> 237 <tests>
200 <test> 238 <test>
239 <param name="database_source_select" value="file" />
201 <param name="database" value="databasetest1.fasta" ftype="fasta" /> 240 <param name="database" value="databasetest1.fasta" ftype="fasta" />
202 <param name="query" value="input83.fasta" ftype="fasta" />
203 <param name="databaseType_select" value="dna" /> 241 <param name="databaseType_select" value="dna" />
204 <param name="queryType" value="dna" /> 242 <param name="queryType" value="dna" />
243 <param name="query" value="input83.fasta" ftype="fasta" />
205 <param name="tileSize" value="11" /> 244 <param name="tileSize" value="11" />
206 <param name="minMatch" value="2" /> 245 <param name="minMatch" value="2" />
207 <param name="stepSize" value="11" /> 246 <param name="stepSize" value="11" />
208 <param name="oneOff" value="false" /> 247 <param name="oneOff" value="false" />
209 <param name="minScore" value="30" /> 248 <param name="minScore" value="30" />