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/lib/galaxy/datatypes/converters/fasta_to_bowtie_base_index_converter.xml

https://bitbucket.org/cistrome/cistrome-harvard/
XML | 22 lines | 20 code | 0 blank | 2 comment | 0 complexity | c3759f18f2a7b85147090513e2f1c31c MD5 | raw file
 1<tool id="CONVERTER_fasta_to_bowtie_base_index" name="Convert FASTA to Bowtie base space Index" version="1.0.0">
 2  <requirements><requirement type='package'>bowtie</requirement></requirements>
 3  <!-- <description>__NOT_USED_CURRENTLY_FOR_CONVERTERS__</description> -->
 4  <!-- Used on the metadata edit page. -->
 5  <requirements>
 6      <requirement type="package">bowtie</requirement>
 7  </requirements>
 8  <command>
 9  mkdir ${output.files_path}
10  &amp;&amp; bowtie-build --quiet
11  -f 
12  $input  ${output.files_path}/${output.metadata.base_name}
13  </command>
14  <inputs>
15    <param name="input" type="data" format="fasta" label="Fasta file"/>
16  </inputs>
17  <outputs>
18    <data name="output" format="bowtie_base_index"/>
19  </outputs>
20  <help>
21  </help>
22</tool>