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comparison blat.xml @ 5:dede60f744f4 draft

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planemo upload commit 2d70129e3c77058bd09e7b0da426b5ee3187cce7
author iuc
date Fri, 23 Jun 2017 23:33:09 -0400
parents 545bc7831814
children 250a7f2b1331
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4:545bc7831814 5:dede60f744f4
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="1.0"> 2 <tool id="ucsc_blat" name="UCSC BLAT Alignment Tool" version="35-0">
3 <description>Standalone blat sequence search command line tool</description> 3 <description>BLAST-like sequence alignment tool</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.0">ucsc_tools_340_for_BLAT</requirement> 5 <requirement type="package" version="35">blat</requirement>
6 </requirements> 6 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #if str($reference_source.reference_source_selector) == "history": 8 #if str($reference_source.reference_source_selector) == "history":
9 #set $reference_fasta_filename = "localref.fa" 9 ## blat depends on file extension
10 #if $reference_source.database.is_of_type("fasta"):
11 #set $reference_fasta_filename = "localref.fa"
12 #elif $reference_source.database.is_of_type("twobit"):
13 #set $reference_fasta_filename = "localref.2bit"
14 #else
15 #set $reference_fasta_filename = "localref"
16 #end if
17
10 ln -s '${reference_source.database}' '${reference_fasta_filename}' && 18 ln -s '${reference_source.database}' '${reference_fasta_filename}' &&
11 #else: 19 #else:
12 #set $reference_fasta_filename = str($reference_source.database.fields.path) 20 #set $reference_fasta_filename = str($reference_source.database.fields.path)
13 #end if 21 #end if
22
14 blat 23 blat
15 #if $noHead == "yes" 24 #if $noHead == "yes"
16 -noHead 25 -noHead
17 #end if 26 #end if
27
18 -q=$query_type 28 -q=$query_type
19 -t=$database_type 29 -t=$database_type
30
20 #if $mask_type.mask == "file.out": 31 #if $mask_type.mask == "file.out":
21 -mask=$mask_type.mask_file 32 -mask='${mask_type.mask_file}'
22 #else: 33 #else:
23 -mask=$mask_type.mask 34 -mask=$mask_type.mask
24 #end if 35 #end if
36
25 '$reference_fasta_filename' 37 '$reference_fasta_filename'
26 '${query}' 38 '${query}'
39
27 output 40 output
28 && sort -k 10,10 -k 12,12n output > '${output_sorted}' 41 && sort -k 10,10 -k 12,12n output > '${output_sorted}'
29 ]]></command> 42 ]]></command>
30 <inputs> 43 <inputs>
31 <conditional name="reference_source"> 44 <conditional name="reference_source">
40 </options> 53 </options>
41 <validator type="no_options" message="A built-in database is not available" /> 54 <validator type="no_options" message="A built-in database is not available" />
42 </param> 55 </param>
43 </when> 56 </when>
44 <when value="history"> 57 <when value="history">
45 <param name="database" type="data" format="fasta,twobit" label="Using database file, either a .fa, .nib or .2bit file" /> 58 <param name="database" type="data" format="fasta, twobit" label="Using database file, either a .fa, .nib or .2bit file" />
46 </when> 59 </when>
47 </conditional> 60 </conditional>
48 <param type="data" name="query" format="fasta,twobit" label="Query data, either a .fa, .nib or .2bit file"/> 61 <param type="data" name="query" format="fasta, twobit" label="Query data, either a .fa, .nib or .2bit file"/>
49 <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t"> 62 <param type="select" name="database_type" format="text" multiple="false" label="database type" help="Choose your database type, the default is dnax" argument="-t">
50 <option value="dna">dna - DNA sequence</option> 63 <option value="dna">dna - DNA sequence</option>
51 <option value="prot">prot - protein sequence</option> 64 <option value="prot">prot - protein sequence</option>
52 <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option> 65 <option value="dnax" selected="true">dnax - DNA sequence translated in six frames to protein</option>
53 </param> 66 </param>