Mercurial > repos > iuc > lorikeet_spoligotype
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planemo upload for repository https://github.com/AbeelLab/lorikeet commit 01d9bfef91bbdfbdaa31c3fc023504181132c001
author | iuc |
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date | Tue, 08 May 2018 04:23:01 -0400 |
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children | f9c37d0b3002 |
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<tool id="lorikeet_spoligotype" name="lorikeet spoligotyping" version="@TOOL_VERSION@+galaxy0" profile="17.01"> <description>M. tuberculosis DNA fingerprinting</description> <macros> <token name="@TOOL_VERSION@">17</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">lorikeet</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ #set $input_file = 'input.' + $input.extension ln -s '${input}' $input_file && lorikeet spoligotype -o '${output_txt}' $input_file #if $spacer_source.source_type == 'file': -s '${spacer_source.spacer}' #end if ]]> </command> <inputs> <param name="input" label="Input sequences" type="data" format="bam" help="Reads of sample(s) being spoligotyped" /> <conditional name="spacer_source"> <param type="select" name="source_type" label="Source for spacer sequences"> <option selected="true" value="builtin">Built-in</option> <option value="file">File with custom spacers</option> </param> <when value="builtin"> </when> <when value="file"> <param argument="--spacer" type="data" format="fasta" label="Spacer file" help="FASTA format file containing customer spacer library" /> </when> </conditional> </inputs> <outputs> <data name="output_txt" format="txt" label="Spoligotype on ${on_string}" /> </outputs> <tests> <test> <param name="input" value="input.bam" ftype="bam" /> <output name="output_txt"> <assert_contents> <has_text text="1111111111 1111111011 1111111111 1100001111 111" /> </assert_contents> </output> </test> <test> <param name="input" value="input.bam" ftype="bam" /> <param name="source_type" value="file" /> <param name="spacer" value="custom_spacers.fasta" ftype="fasta" /> <output name="output_txt"> <assert_contents> <has_text text="1111111111 0000000000 0000000000 0000000000 000" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ Lorikeet_ is a tool for digital spoligotyping_ of M. tuberculosis strains from Illumina data. Input is a file of Illumina reads and output is a spoligotyping report. While by default lorikeet uses its own built-in collection of spacer sequences, a custom file of spacers can be provided if necessary. .. _Lorikeet: https://github.com/AbeelLab/lorikeet .. _spoligotyping: https://link.springer.com/protocol/10.1007%2F978-1-60327-999-4_10 ]]> </help> <citations> <citation type="doi">10.1371/journal.pmed.1001880</citation> </citations> </tool>