Mercurial > repos > iuc > obi_illumina_pairend
comparison illuminapairedend.xml @ 4:8cb6bd511879 draft default tip
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 |