Mercurial > repos > iuc > obi_sort
diff obisort.xml @ 0:aca6a8c9cf83 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2
author | iuc |
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date | Wed, 12 Apr 2017 17:38:00 -0400 |
parents | |
children | 0de27b538106 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/obisort.xml Wed Apr 12 17:38:00 2017 -0400 @@ -0,0 +1,67 @@ +<tool id="obi_sort" name="obisort" version="@WRAPPER_VERSION@"> + <description>sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + + <command> + + <![CDATA[ + obisort + -k '$key' + ${reverse} + '$input' > '$output' + ]]> + + </command> + + <inputs> + <param name="input" type="data" format="fastq,fasta,txt,tabular" label="Input sequences file" /> + <param name="key" type="text" label="key" /> + <param name="reverse" type="boolean" checked="false" truevalue="-r" falsevalue="" label="sorts in reverse order?" /> + <param name="out_format" type="select" label="Output data type"> + <option value="fasta">fasta</option> + <option value="fastq">fastq</option> + </param> + + </inputs> + <outputs> + <data format="fastq" name="output" label="output with ${tool.name} on ${on_string}" > + <change_format> + <when input="out_format" value="fasta" format="fasta" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input" value="output_obiclean_advanced.fasta" /> + <param name="key" value="count"/> + <param name="reverse" value="False"/> + <param name="out_format" value="fasta"/> + <output name="output" file="output_obisort.fasta" ftype="fasta"/> + </test> + <test> + <param name="input" value="output_obiclean_advanced.fasta" /> + <param name="key" value="count"/> + <param name="reverse" value="True"/> + <param name="out_format" value="fastq"/> + <output name="output" file="output_obisort.fastq" ftype="fastq"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +obisort sorts sequence records according to the value of a given attribute, which can be either numeric or alphanumeric. + +@OBITOOLS_LINK@ + + ]]> + + </help> + <expand macro="citation" /> +</tool>