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comparison jellyfish.xml @ 2:dcd30574a456 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jellyfish commit aa8360cb3ec9faf1488938a430855977632706ff
author iuc
date Sun, 07 Jan 2024 16:28:53 +0000
parents 11658afb8c87
children
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1:11658afb8c87 2:dcd30574a456
1 <tool id="jellyfish" name="jellyfish" version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="jellyfish" name="jellyfish" version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01">
2 <macros> 2 <macros>
3 <token name="@WRAPPER_VERSION@">2.3.0</token> 3 <token name="@WRAPPER_VERSION@">2.3.0</token>
4 <token name="@VERSION_SUFFIX@">galaxy0</token> 4 <token name="@VERSION_SUFFIX@">galaxy1</token>
5 </macros> 5 </macros>
6 <xrefs> 6 <xrefs>
7 <xref type="bio.tools">Jellyfish</xref> 7 <xref type="bio.tools">Jellyfish</xref>
8 </xrefs> 8 </xrefs>
9 <requirements> 9 <requirements>
12 <command detect_errors="exit_code"><![CDATA[ 12 <command detect_errors="exit_code"><![CDATA[
13 jellyfish 13 jellyfish
14 #if $commands.command == "count": 14 #if $commands.command == "count":
15 count 15 count
16 --mer-len $commands.mer_len 16 --mer-len $commands.mer_len
17 --size $commands.size 17 --size ${commands.size}M
18 #if $commands.counter_len: 18 #if $commands.counter_len:
19 --counter-len $commands.counter_len 19 --counter-len $commands.counter_len
20 #end if 20 #end if
21 $commands.canonical 21 $commands.canonical
22 #if $commands.bloom.filters == "bc": 22 #if $commands.bloom.filters == "bc":
101 <option value="query"/> --> 101 <option value="query"/> -->
102 </param> 102 </param>
103 <when value="count"> 103 <when value="count">
104 <param name="input" type="data" format="fasta,fastq,fastqsanger" label="Input data file"/> 104 <param name="input" type="data" format="fasta,fastq,fastqsanger" label="Input data file"/>
105 <param argument="--mer-len" type="integer" value="20" min="1" label="Length of mer" /> 105 <param argument="--mer-len" type="integer" value="20" min="1" label="Length of mer" />
106 <param argument="--size" type="integer" value="32" min="1" label="Initial hash size" /> 106 <param argument="--size" type="integer" value="32" min="1" label="Initial hash size in Million (M)" />
107 <param argument="--counter-len" type="integer" min="1" optional="true" label="Counter Length in bits" /> 107 <param argument="--counter-len" type="integer" min="1" optional="true" label="Counter Length in bits" />
108 <param argument="--canonical" type="boolean" truevalue="--canonical" falsevalue="" label="Count both strand and canonical representation" /> 108 <param argument="--canonical" type="boolean" truevalue="--canonical" falsevalue="" label="Count both strand and canonical representation" />
109 <conditional name="bloom"> 109 <conditional name="bloom">
110 <param name="filters" type="select" label="Use bloom filters"> 110 <param name="filters" type="select" label="Use bloom filters">
111 <option value="default">Default</option> 111 <option value="default">Default</option>