annotate pepnovo_adapter.xml @ 6:42b843627623 draft default tip

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<tool id="pepnovo_adapter" version="0.1.0" name="PepNovo (OpenMS)">
  <description>
  </description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expnad macro="stdio" />
  <expand macro="requires">
    <requirement type="package">pepnovo</requirement>
  </expand>
  <command interpreter="python">
    openms_wrapper.py 
#if $input_block.do_clean
    --executable 'FileConverter' --config $inputConfig
#end if
    --executable 'PepNovoAdapter' --config $config
  </command>
  <configfiles>
    <configfile name="config">[simple_options]
#if $input_block.do_clean
in=input.mzXML
#else
in=${input_block.input1}
#end if
out=${out}
model_directory=@PEPNOVO_MODELS_PATH@
pepnovo_executable=@WHICH(PepNovo)@
temp_data_directory=.
model=${model}
digest=${digest}
num_solutions=${num_solutions}
#if str($corrections) != "none"
correct_pm=true
#end if
#if str($corrections) == "mass"
use_spectrum_charge=true
#end if
#if str($corrections) == "mz"
use_spectrum_mz=true
#end if
$quality_filter
#if $override_pm.do_override
pm_tolerance=${override_pm.percursor_tolerance}
#end if
#if $override_fragment.do_override
fragment_tolerance=${override_fragment.fragment_tolerance}
#end if
#set $fixed_mods_str=",".join([str($fixed_mod.fixed_mod) for $fixed_mod in $fixed_mods])
#if $fixed_mods_str
fixed_modifications=$fixed_mods_str
#end if
#set $variable_mods_str=",".join([str($variable_mod.variable_mod) for $variable_mod in $variable_mods])
#if $variable_mods_str
variable_modifications=$variable_mods_str
#end if
</configfile>
    <configfile name="inputConfig">[simple_options]
in=${input_block.input1}
in_type=${input_block.input1.ext}
out=input.mzXML
out_type=mzXML
</configfile>
  </configfiles>
  <inputs>
    <conditional name="input_block">
      <param name="do_clean" type="boolean" label="Process input peak list" description="The version of PepNovo used by this tool takes only mzXML files and even then fails to parse many valid such files. Enabling this option will run the input peak list (mzXML or otherwise) through the OpenMS FileConverter application to hopefully produce an mzXML file suitable for PepNovo." />
      <when value="true">
        <param name="input1" type="data" format="mzxml,mzml,mgf,ms2" label="Input peak list" />
      </when>
      <when value="false">
        <param name="input1" type="data" format="mzxml" label="Input peak list" />
      </when>
    </conditional>
    <param name="model" type="select" label="Model">
      <options from_file="pepnovo_models.loc">
        <column name="name" index="0" />
        <column name="value" index="0" />
      </options>
    </param>
    <param name="digest" type="select" label="Digest"> 
      <option value="TRYPSIN">Trypsin</option>
      <option value="NON_SPECIFIC">Non-specific</option>
    </param>
    <param name="corrections" type="select" label="Spectrum adjustments">
      <option value="none">None.</option>
      <option value="both">Find optimal precursor m/z and charge values.</option>
      <option value="mz">Find optimal precursor m/z values.</option>
      <option value="charge">Find optimal charge values.</option>
    </param>
    <repeat name="fixed_mods" title="Fixed Modification">
      <param name="fixed_mod" type="select" label="Fixed Modification">
        <options from_file="openms_mods.loc">
          <column name="name" index="0" />
          <column name="value" index="0" />
        </options>
      </param>
    </repeat>
    <repeat name="variable_mods" title="Variable Modification">
      <param name="variable_mod" type="select" label="Variable Modification">
        <options from_file="openms_mods.loc">
          <column name="name" index="0"/>
          <column name="value" index="0" />
        </options>
      </param>
    </repeat>
    <param name="quality_filter" type="boolean" checked="true" label="Filter low quality spectra" truevalue="no_quality_filter=true" falsevalue=""/>
    <conditional name="override_pm">
      <param name="do_override" type="boolean" label="Override model's percursor mass tolerance" />
      <when value="true">
        <param name="percursor_tolerance" type="float" label="Precursor mass tolerance (Daltons)" help="Must between 0 and 5.0. Set to -1.0 to use model default." value="-1.0">
          <validator type="in_range" min="-1.0" max="5.0" />
        </param>
      </when>
      <when value="false">
      </when>
    </conditional>
    <conditional name="override_fragment">
      <param name="do_override" type="boolean" label="Override model's fragment tolerance" />
      <when value="true">
        <param name="fragment_tolerance" type="float" label="Fragment tolerance (Daltons)" help="Must between 0 and 0.75. Set to -1.0 to use model default." value="-1.0">
          <validator type="in_range" min="-1.0" max="0.75" />
        </param>
      </when>
      <when value="false">
      </when>
    </conditional>
    <param name="num_solutions" type="integer" label="Number of Solutions" value="20">
      <validator type="in_range" message="1 &lt;= Number of Solutions &lt;= 2000" min="1" max="2000"/>
    </param>
  </inputs>
  <outputs>
    <data format="idxml" name="out" />
  </outputs>
  <help>
**What it does**

De novo peptide sequencing of mass spectrometry data. 

More information and publications on PepNovo can be found at the following site: http://proteomics.ucsd.edu/Software/PepNovo.html.

**Citation**

For the underlying tool, please cite ``Marc Sturm, Andreas Bertsch, Clemens Gröpl, Andreas Hildebrandt, Rene Hussong, Eva Lange, Nico Pfeifer, Ole Schulz-Trieglaff, Alexandra Zerck, Knut Reinert, and Oliver Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry. BMC Bioinformatics 9: 163. doi:10.1186/1471-2105-9-163.`` and ``PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Frank, A. and Pevzner, P. Analytical Chemistry 77:964-973, 2005.``.

If you use this tool in Galaxy, please cite Chilton J, et al. https://bitbucket.org/galaxyp/galaxyp-toolshed-openms
  </help>
</tool>