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1 <tool id="pyfaidx" name="pyfaidx" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>efficient FASTA indexing</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 #if $input.is_of_type('fasta.gz'):
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9 gunzip -c '$input' > 'input.fasta' &&
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10 #else:
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11 ln -s '$input' 'input.fasta' &&
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12 #end if
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13 faidx -i chromsizes 'input.fasta' > '$output'
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14 ]]></command>
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15 <inputs>
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16 <param name="input" type="data" format="fasta,fasta.gz" label="Assembled FASTA file"/>
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17 </inputs>
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18 <outputs>
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19 <data name="output" format="fasta"/>
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20 </outputs>
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21 <tests>
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22 <test>
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23 <param name="input" value="input.fasta.gz" ftype="fasta.gz"/>
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24 <output name="output" ftype="fasta">
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25 <assert_contents>
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26 <has_size value="51690"/>
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27 <has_text text=">contig_10"/>
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28 <has_text text=">contig_7"/>
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29 </assert_contents>
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30 </output>
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31 </test>
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32 </tests>
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33 <help>
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34 **What it does**
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35
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36 Runs faidx to index the input FASTA file.
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37 </help>
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38 <expand macro="citations"/>
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39 </tool>
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40
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