Mercurial > repos > iuc > obi_illumina_pairend

comparison illuminapairedend.xml @ 4:8cb6bd511879 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44
author iuc
date Wed, 20 Mar 2024 13:17:09 +0000
parents 83fbdf93d51e
children
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3:83fbdf93d51e 4:8cb6bd511879
1 <tool id="obi_illumina_pairend" name="Illuminapairedend" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="obi_illumina_pairend" name="Illuminapairedend" version="@TOOL_VERSION@" profile="@PROFILE@">
2 <description>Construct consensus reads from Illumina pair-end reads</description> 2 <description>Construct consensus reads from Illumina pair-end reads</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
6 <expand macro="requirements"/> 7 <expand macro="requirements"/>
7 <expand macro="stdio"/> 8 <expand macro="stdio"/>
8 <command> 9 <command>
9 <![CDATA[ 10 <![CDATA[
10 #if $inputfastq3p.ext.endswith(".gz") 11 #if $inputfastq3p.ext.endswith(".gz")
45 <outputs> 46 <outputs>
46 <data name="output" format_source="inputfastq3p" label="${tool.name} on ${on_string}: assembly results" /> 47 <data name="output" format_source="inputfastq3p" label="${tool.name} on ${on_string}: assembly results" />
47 </outputs> 48 </outputs>
48 49
49 <tests> 50 <tests>
50 <test> 51 <test expect_num_outputs="1">
51 <param name="inputfastq3p" value="wolf_small.F.fastq" ftype="fastqsanger" /> 52 <param name="inputfastq3p" value="wolf_small.F.fastq" ftype="fastqsanger" />
52 <param name="inputfastq5p" value="wolf_small.R.fastq" ftype="fastqsanger" /> 53 <param name="inputfastq5p" value="wolf_small.R.fastq" ftype="fastqsanger" />
53 <param name="score" value="40.0" /> 54 <param name="score" value="40.0" />
54 <output name="output" file="illuminapairedend.output.fastq" ftype="fastqsanger" /> 55 <output name="output" file="illuminapairedend.output.fastq" ftype="fastqsanger" />
55 </test> 56 </test>
56 <test> 57 <test expect_num_outputs="1">
57 <param name="inputfastq3p" value="wolf_small.F.fastq.gz" ftype="fastqsanger.gz" /> 58 <param name="inputfastq3p" value="wolf_small.F.fastq.gz" ftype="fastqsanger.gz" />
58 <param name="inputfastq5p" value="wolf_small.R.fastq.gz" ftype="fastqsanger.gz" /> 59 <param name="inputfastq5p" value="wolf_small.R.fastq.gz" ftype="fastqsanger.gz" />
59 <param name="score" value="40.0" /> 60 <param name="score" value="40.0" />
60 <output name="output" file="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz" decompress="true"/> 61 <output name="output" file="illuminapairedend.output.fastq.gz" ftype="fastqsanger.gz" decompress="true"/>
61 </test> 62 </test>
91 ]]> 92 ]]>
92 </help> 93 </help>
93 <expand macro="citation" /> 94 <expand macro="citation" />
94 95
95 </tool> 96 </tool>
97