comparison Decharger.xml @ 11:2378124da7c4 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5

10:9fb4bc0c5288

    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>Decharger

#if $param_in:
  -in $param_in
#end if
#if $param_out_cm:

#end if
    #if $adv_opts.param_algorithm_FeatureDeconvolution_verbose_level:
  -algorithm:FeatureDeconvolution:verbose_level $adv_opts.param_algorithm_FeatureDeconvolution_verbose_level
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="featurexml" optional="False" label="input file" help="(-in) "/>
    <param name="param_algorithm_FeatureDeconvolution_charge_min" type="integer" value="1" label="Minimal possible charge" help="(-charge_min) "/>
    <param name="param_algorithm_FeatureDeconvolution_charge_max" type="integer" value="10" label="Maximal possible charge" help="(-charge_max) "/>
    <param name="param_algorithm_FeatureDeconvolution_charge_span_max" type="integer" min="1" optional="True" value="4" label="Maximal range of charges for a single analyte, i.e" help="(-charge_span_max) observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge"/>

    <data name="param_outpairs" format="consensusxml"/>
  </outputs>
  <help>Decharges and merges different feature charge variants of the same peptide.


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_Decharger.html</help>
</tool>

11:2378124da7c4

    <import>macros.xml</import>
  </macros>
  <expand macro="references"/>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[Decharger

#if $param_in:
  -in $param_in
#end if
#if $param_out_cm:

#end if
    #if $adv_opts.param_algorithm_FeatureDeconvolution_verbose_level:
  -algorithm:FeatureDeconvolution:verbose_level $adv_opts.param_algorithm_FeatureDeconvolution_verbose_level
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="featurexml" optional="False" label="input file" help="(-in) "/>
    <param name="param_algorithm_FeatureDeconvolution_charge_min" type="integer" value="1" label="Minimal possible charge" help="(-charge_min) "/>
    <param name="param_algorithm_FeatureDeconvolution_charge_max" type="integer" value="10" label="Maximal possible charge" help="(-charge_max) "/>
    <param name="param_algorithm_FeatureDeconvolution_charge_span_max" type="integer" min="1" optional="True" value="4" label="Maximal range of charges for a single analyte, i.e" help="(-charge_span_max) observing q1=[5,6,7] implies span=3. Setting this to 1 will only find adduct variants of the same charge"/>

    <data name="param_outpairs" format="consensusxml"/>
  </outputs>
  <help>Decharges and merges different feature charge variants of the same peptide.


For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_Decharger.html</help>
</tool>