<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook V4.1//EN">
<refentry>
  <refentryinfo>
    <date>05 december 2013</date>
  </refentryinfo>
  <refmeta>
    <refentrytitle>
      <application>IDCONVERT</application>
    </refentrytitle>
    <manvolnum>1</manvolnum>
    <refmiscinfo>idconvert</refmiscinfo>
  </refmeta>
  <refnamediv>
    <refname>
      <application>idconvert</application>
    </refname>
    <refpurpose>
      Convert mass spectrometry identification file formats.
    </refpurpose>
  </refnamediv>
  <refsynopsisdiv>
    <cmdsynopsis>
      <command>idconvert</command>
      <arg><option><replaceable class="parameter">options</replaceable></option></arg>
      <arg><option><replaceable class="parameter">filemasks</replaceable></option></arg>
    </cmdsynopsis>
  </refsynopsisdiv>
  <refsect1>
    <title>DESCRIPTION</title>
    <para>
      This manual page documents briefly
      the <command>idconvert</command> software shipped within the
      <filename>libpwiz-tools</filename> package. This program allows
      one to convert mass spectrometry protein identification data
      files from one format to another.
    </para>
  </refsect1>
  <refsect1>
    <title>OPTIONS</title>
    <variablelist>

      <varlistentry>
	<term>-v | --verbose</term>
	<listitem>
	  <para>
	    Display detailed processing progress information.
	  </para>
	</listitem>
      </varlistentry>

      <varlistentry>
	<term>-f | --filelist <replaceable class="parameter">filename</replaceable></term>
	<listitem>
	  <para>
	    Uses the contents of <replaceable class="parameter">filename</replaceable> which lists filenames.
	  </para>
	</listitem>      
      </varlistentry>

      <varlistentry>
	<term>-o | --outdir <replaceable class="parameter">dir</replaceable></term>
	<listitem>
	  <para>
	    Set the output directory ('-' for stdout) to <replaceable class="parameter">dir</replaceable>. By default, the output directory is '.' (that is, the current working directory).
	  </para>
	</listitem>
      </varlistentry>
      
      <varlistentry>
	<term>-c | --config <replaceable class="parameter">filename</replaceable></term>
	<listitem>
	  <para>
	    Set the configuration file to <replaceable class="parameter">filename</replaceable>.
	  </para>
	</listitem>
      </varlistentry>
      
      <varlistentry>
	<term>-e | --ext <replaceable class="parameter">ext</replaceable></term>
	<listitem>
	  <para>
	    Set the extension of the output files
	    to <replaceable class="parameter">ext</replaceable>. Can
	    be mzid or pepXML or txt.
	  </para>
	</listitem>
      </varlistentry>

      <varlistentry>
	<term>--mzIdentML</term>
	<listitem>
	  <para>
	    Write <filename>mzIdentML</filename> format (default).
	  </para>
	</listitem>
      </varlistentry>

      <varlistentry>
	<term>--pepXML</term>
	<listitem>
	  <para>
	    Write <filename>pepXML</filename> format.
	  </para>
	</listitem>
      </varlistentry>

      <varlistentry>
	<term>--text</term>
	<listitem>
	  <para>
	    Write hierarchical <filename>text</filename> format.
	  </para>
	</listitem>
      </varlistentry>
    </variablelist>

  </refsect1>
  <refsect1>
    <title>EXAMPLES</title>
    <para>
      Convert sequest.pepXML to sequest.mzid
    </para>
    <para>
      <command>idconvert sequest.pepXML</command>
    </para>

    <para>
      Convert mascot.mzid to mascot.pepXML
    </para>
    <para>
      <command>idconvert mascot.mzid --pepXML</command>
    </para>

    <para>
      Use a configuration file
    </para>
    <para>
      <command>idconvert xtandem.pep.xml -c config.txt</command>
    </para>
  </refsect1>

  <refsect1>
    <title>RETURN VALUE</title>
    <para>
      The number of failed files.
    </para>
  </refsect1>

  <refsect1>
    <title>AUTHOR</title>
    <para>
      <author>
	<firstname>Filippo</firstname>
	<surname>Rusconi &lt;lopippo@debian.org&gt;</surname>
	<authorblurb>
	  <para>
	    This manual page was written by Filippo Rusconi
	    &lt;lopippo@debian.org&gt; (initial writing 05 december
	    2013). Permission is granted to copy, distribute and/or
	    modify this document under the terms of the GNU General
	    Public License, Version 3, published by the Free Software
	    Foundation.
	  </para>
	  
	  <para>
	    On a Debian system the complete text of the GNU General
	    Public License version 3 can be found in the file
	    `<filename>/usr/share/common-licenses/GPL\-3</filename>'.
	  </para>

	</authorblurb>
      </author>
    </para>
  </refsect1>
</refentry>









