implementation of output prefix parameters

[bernt-matthias]

as discussed in #4404

implementation for SeedListGenerator currently only works for consensusXML input. For this tool one could think about to have the -out and the -out_prefix that could be used exclusively. for the -out_prefix parameter a question would be how the names should be generated for the other input types.

TODOs:

• CTD changes

[jpfeuffer]

This looks like a great start. Indeed the CTD changes are missing, but at least the prefix type already exists there. I will try to add to this PR when I find time again.

[timosachsenberg]

any update here?

[timosachsenberg]

/rebase

[timosachsenberg]

Tests pass and ini ctd contain the entry:
ini

      <ITEM name="out_prefix" value="" type="output-prefix" description="Output file prefix" required="true" advanced="false" supported_formats="*.featureXML" />

CTD

<?xml version="1.0" encoding="UTF-8"?>
<tool ctdVersion="1.7" version="2.7.0-pre-topic-output-prefix-2022-01-07" name="SeedListGenerator" docurl="http://www.openms.de/doxygen/nightly/html/TOPP_SeedListGenerator.html" category="Quantitation" >
<description><![CDATA[Generates seed lists for feature detection.]]></description>
<manual><![CDATA[Generates seed lists for feature detection.]]></manual>
<citations>
  <citation doi="10.1038/nmeth.3959" url="" />
</citations>
<PARAMETERS version="1.7.0" xsi:noNamespaceSchemaLocation="https://raw.githubusercontent.com/OpenMS/OpenMS/develop/share/OpenMS/SCHEMAS/Param_1_7_0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <NODE name="SeedListGenerator" description="Generates seed lists for feature detection.">
    <ITEM name="version" value="2.7.0-pre-topic-output-prefix-2022-01-07" type="string" description="Version of the tool that generated this parameters file." required="false" advanced="true" />
    <NODE name="1" description="Instance &apos;1&apos; section for &apos;SeedListGenerator&apos;">
      <ITEM name="in" value="" type="input-file" description="Input file (see below for details)" required="true" advanced="false" supported_formats="*.mzML,*.idXML,*.featureXML,*.consensusXML" />
      <ITEM name="out_prefix" value="" type="output-prefix" description="Output file prefix" required="true" advanced="false" supported_formats="*.featureXML" />
      <ITEM name="use_peptide_mass" value="false" type="bool" description="[idXML input only] Use the monoisotopic mass of the best peptide hit for the m/z position (default: use precursor m/z)" required="false" advanced="false" />
      <ITEM name="log" value="" type="string" description="Name of log file (created only when specified)" required="false" advanced="true" />
      <ITEM name="debug" value="0" type="int" description="Sets the debug level" required="false" advanced="true" />
      <ITEM name="threads" value="1" type="int" description="Sets the number of threads allowed to be used by the TOPP tool" required="false" advanced="false" />
      <ITEM name="no_progress" value="false" type="bool" description="Disables progress logging to command line" required="false" advanced="true" />
      <ITEM name="force" value="false" type="bool" description="Overrides tool-specific checks" required="false" advanced="true" />
      <ITEM name="test" value="false" type="bool" description="Enables the test mode (needed for internal use only)" required="false" advanced="true" />
    </NODE>
  </NODE>
</PARAMETERS>
</tool>