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comparison blat.xml @ 12:e79965d0351c draft default tip

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planemo upload commit 6358ce7c332f42526423d365f06516983ca677a0
author iuc
date Sat, 03 Dec 2022 10:38:40 +0000
parents 2a89f630fa85
children
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11:2a89f630fa85 12:e79965d0351c
1 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>BLAST-like sequence alignment tool</description> 2 <description>BLAST-like sequence alignment tool</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">377</token> 4 <token name="@TOOL_VERSION@">377</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 6
7 <xml name="mask_cond" tokens="maskarg,label,help"> 7 <xml name="mask_cond" tokens="maskarg,label,help">
8 <conditional name="@MASKARG@_type"> 8 <conditional name="@MASKARG@_type">
9 <param argument="-@MASKARG@" type="select" label="@LABEL@" help="@HELP@"> 9 <param argument="-@MASKARG@" type="select" label="@LABEL@" help="@HELP@">
10 <option value="" selected="true">No masking</option> 10 <option value="" selected="true">No masking</option>
28 <requirement type="package" version="@TOOL_VERSION@">ucsc-blat</requirement> 28 <requirement type="package" version="@TOOL_VERSION@">ucsc-blat</requirement>
29 </requirements> 29 </requirements>
30 <command detect_errors="exit_code"><![CDATA[ 30 <command detect_errors="exit_code"><![CDATA[
31 #if str($reference_source.reference_source_selector) == "history": 31 #if str($reference_source.reference_source_selector) == "history":
32 ## blat depends on file extension 32 ## blat depends on file extension
33 #if $reference_source.database.is_of_type("fasta"): 33 #if $reference_source.database.is_of_type("fasta.gz"):
34 #set $reference_fasta_filename = "localref.fa.gz"
35 #elif $reference_source.database.is_of_type("fasta"):
34 #set $reference_fasta_filename = "localref.fa" 36 #set $reference_fasta_filename = "localref.fa"
35 #elif $reference_source.database.is_of_type("twobit"): 37 #elif $reference_source.database.is_of_type("twobit"):
36 #set $reference_fasta_filename = "localref.2bit" 38 #set $reference_fasta_filename = "localref.2bit"
37 #else 39 #else
38 #set $reference_fasta_filename = "localref" 40 #set $reference_fasta_filename = "localref"
39 #end if 41 #end if
40 ln -s '$reference_source.database' '$reference_fasta_filename' && 42 ln -s '$reference_source.database' '$reference_fasta_filename' &&
41 #else: 43 #else:
42 #set $reference_fasta_filename = str($reference_source.database.fields.path) 44 #set $reference_fasta_filename = str($reference_source.database.fields.path)
43 #end if 45 #end if
46
47 ## blat depends on file extension
48 #if $query.is_of_type("fasta.gz"):
49 #set $query_filename = "query.fa.gz"
50 #elif $query.is_of_type("fasta"):
51 #set $query_filename = "query.fa"
52 #elif $query.is_of_type("twobit"):
53 #set $query_filename = "query.2bit"
54 #else
55 #set $query_filename = "query"
56 #end if
57 ln -s '$query' '$query_filename' &&
44 58
45 blat 59 blat
46 -q=$query_type 60 -q=$query_type
47 -t=$database_type 61 -t=$database_type
48 ## Basic alignment parameters 62 ## Basic alignment parameters
98 112
99 #if str($dots) 113 #if str($dots)
100 -dots=$dots 114 -dots=$dots
101 #end if 115 #end if
102 '$reference_fasta_filename' 116 '$reference_fasta_filename'
103 '$query' 117 '$query_filename'
104 -out=$out 118 -out=$out
105 '$output' 119 '$output'
106 ]]></command> 120 ]]></command>
107 <inputs> 121 <inputs>
108 <conditional name="reference_source"> 122 <conditional name="reference_source">
119 </options> 133 </options>
120 <validator type="no_options" message="A built-in database is not available" /> 134 <validator type="no_options" message="A built-in database is not available" />
121 </param> 135 </param>
122 </when> 136 </when>
123 <when value="history"> 137 <when value="history">
124 <param name="database" type="data" format="fasta,twobit" label="Using database file, either a .fa, .nib or .2bit file" /> 138 <param name="database" type="data" format="fasta,fasta.gz,twobit" label="Using database file, either a fasta, fasta.gz or twobit dataset" />
125 </when> 139 </when>
126 </conditional> 140 </conditional>
127 <param name="query" type="data" format="fasta, twobit" label="Query data, either a .fa, .nib or .2bit file"/> 141 <param name="query" type="data" format="fasta,fasta.gz,twobit" label="Query data, either a fasta, fasta.gz or twobit dataset"/>
128 <param argument="-t" name="database_type" type="select" format="txt" multiple="false" label="database type" help="Choose your database type, the default is dnax"> 142 <param argument="-t" name="database_type" type="select" format="txt" multiple="false" label="database type" help="Choose your database type, the default is dnax">
129 <option value="dna" selected="true">dna - DNA sequence</option> 143 <option value="dna" selected="true">dna - DNA sequence</option>
130 <option value="prot">prot - protein sequence</option> 144 <option value="prot">prot - protein sequence</option>
131 <option value="dnax">dnax - DNA sequence translated in six frames to protein</option> 145 <option value="dnax">dnax - DNA sequence translated in six frames to protein</option>
132 </param> 146 </param>
257 <has_text text="-tileSize=" negate="true"/> 271 <has_text text="-tileSize=" negate="true"/>
258 <has_text text="-stepSize=" negate="true"/> 272 <has_text text="-stepSize=" negate="true"/>
259 <has_text text="-mask='/"/> 273 <has_text text="-mask='/"/>
260 </assert_command> 274 </assert_command>
261 </test> 275 </test>
262 </tests> 276 <!-- tiny test data from https://davetang.org/muse/2012/05/15/using-blat/ -->
277 <test>
278 <conditional name="reference_source">
279 <param name="reference_source_selector" value="history" />
280 <param name="database" value="mini-db.fa.gz" ftype="fasta.gz" />
281 </conditional>
282 <param name="query" value="mini-query.fa.gz" ftype="fasta.gz"/>
283 <param name="minScore" value="0" />
284 <section name="adv_align">
285 <param name="stepSize" value="1"/>
286 </section>
287 <param name="out" value="psl" ftype="tabular" />
288 <output name="output">
289 <assert_contents>
290 <has_n_lines n="7"/>
291 </assert_contents>
292 </output>
293 <assert_command>
294 <has_text text="-minScore=0"/>
295 <has_text text="-stepSize=1"/>
296 </assert_command>
297 </test> </tests>
263 <help> 298 <help>
264 <![CDATA[ 299 <![CDATA[
265 BLAT 300 BLAT
266 ==== 301 ====
267 BLAT is a bioinformatics software a tool which performs rapid sequence alignments (mRNA/DNA and cross-species protein). 302 BLAT is a bioinformatics software a tool which performs rapid sequence alignments (mRNA/DNA and cross-species protein).