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<?xml version="1.0" encoding="ISO-8859-1"?>
<!-- XML Authors: Herve Menager                                                  -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris.         -->
<!-- Distributed under LGPLv2 Licence. Please refer to the COPYING.LIB document. -->
<program>
  <head>
    <name>fastaRename</name>
    <version>1.0</version>
    <doc>
      <title>fasta header shortener</title>
      <description>
        <text lang="en">helps out with the 10-character limit of the PHYLIP-PHYML formats</text>
      </description>
      <authors>Bertrand NĂ©ron</authors>
      <comment>
         <div xmlns="http://www.w3.org/1999/xhtml">
            Due to an incompatibility between the PHYLIP format and phyml and morePhyml named rules, 
            the using of long identifier in phyml or morePhyml failed. We proposed the following workaround:
            <ol>
               <li>use fastaRename to generate an alignment with short ID and a file of ID mapping</li>
               <li>perform your analysis with the alignment with short id</li>
               <li>replace the short IDs in your tree (in NEWICK format) with nw_rename and the file of IDs mapping generated at the step 1.</li> 
            </ol>
         </div>
      </comment>   
    </doc>
    <category>sequence:formatter</category>
    <command>fastaRename</command>
  </head>
  <parameters>
    <parameter ismandatory="1" issimple="1">
      <name>input</name>
      <prompt lang="en">Input sequence file</prompt>
      <example>&gt;VERY_VERY_LONG_ID1
---AAAAGAAAATAGTNNTTCTGGTTGATCCTGCCAGAGGCCATTGCTATCAGGGTNTGACTAAGCCATGCGAGTCGAGAGGTGT-------AAGACCTCGGC
ATACTGCTCAGTAACAC
>&gt;VERY_VERY_LONG_ID2
--------------------------AACGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGCGAAAGGGG--GCTTCGGCGGGGGGAGTAGAGTGGC
GCACGGGTGAGTAACGC
>&gt;VERY_VERY_LONG_ID3
TTATGGAGAGTTTGATCCTGGCTCAGAGTGAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGATGAAGCTTTTAGCTTGCTAGAAGTGGATTAGTGGC
GCACGGGTGAGTAATGC
</example>
      <type>
        <datatype>
          <class>Alignment</class>
        </datatype>
        <dataFormat>FASTA</dataFormat>
      </type>
      <format>
        <code proglang="perl">" $value"</code>
        <code proglang="python">" " + str(value)</code>
      </format>
      <argpos>1</argpos>
    </parameter>
    <parameter isout="1">
      <name>output_fasta</name>
      <prompt lang="en">Output file with renamed headers</prompt>
      <comment>type any kind of text</comment>
      <example>example text</example>
      <type>
        <datatype>
          <class>Alignment</class>
        </datatype>
        <dataFormat>FASTA</dataFormat>
      </type>
      <filenames>
        <code proglang="perl">"*.rename.fasta"</code>
        <code proglang="python">"*.rename.fasta"</code>
      </filenames>
    </parameter>
    <parameter isout="1">
      <name>output_map</name>
      <prompt lang="en">Output file header map</prompt>
      <type>
        <datatype>
          <class>ID_Mapping</class>
          <superclass>AbstractText</superclass>
        </datatype>
      </type>
      <filenames>
        <code proglang="perl">"*.map"</code>
        <code proglang="python">"*.map"</code>
      </filenames>
    </parameter>
  </parameters>
</program>