Mercurial > repos > mbernt > fasta_regex_finder

comparison fastaregexfinder.xml @ 1:9a811adb714f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics-cafe commit c318cd3f894f89c13d7eb257678673da70f72212
author iuc
date Wed, 25 Jan 2023 14:03:52 +0000
parents 269c627ae9f4
children
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0:269c627ae9f4 1:9a811adb714f
1 <tool id="fasta_regex_finder" name="fasta_regex_finder" version="0.1.0"> 1 <tool id="fasta_regex_finder" name="Fasta regular expression finder" version="0.1.0">
2 <description> 2 <description>
3 Search in fasta for regexp match 3 Search in fasta for regexp match
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="3.8">python</requirement>
6 </requirements> 7 </requirements>
7 <version_command>python $__tool_directory__/fastaregexfinder.py --version</version_command> 8 <version_command>python '$__tool_directory__/fastaregexfinder.py' --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 python $__tool_directory__/fastaregexfinder.py 10 python '$__tool_directory__/fastaregexfinder.py'
10 --fasta "$input" 11 --fasta '$input'
11 --regex "$regex" 12 --regex '$regex'
12 #if $settings.advanced == "advanced" 13 #if $settings.advanced == "advanced"
13 $settings.matchcase 14 $settings.matchcase
14 $settings.noreverse 15 $settings.noreverse
15 --maxstr $settings.maxstr 16 --maxstr $settings.maxstr
16 #if $settings.seqnames != "" 17 #if $settings.seqnames != ""
17 --seqnames $settings.seqnames 18 --seqnames $settings.seqnames
18 #end if 19 #end if
19 #end if 20 #end if
20 --quiet 21 --quiet
21 > $output 22 > '$output'
22 ]]></command> 23 ]]></command>
23 <inputs> 24 <inputs>
24 <param type="data" name="input" format="fasta" /> 25 <param type="data" name="input" format="fasta" />
25 <param name="regex" size="30" type="text" value="([gG]{3,}\w{1,7}){3,}[gG]{3,}" label="Regular expression" help="(--regex)"> 26 <param name="regex" size="30" type="text" value="([gG]{3,}\w{1,7}){3,}[gG]{3,}" label="Regular expression" help="(--regex)">
26 <sanitizer> 27 <sanitizer>