comparison MascotAdapter.xml @ 7:fd960d61b64d draft

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

6:83b02507dcd2

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

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

#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="txt" label="input file in mzData format" help="(-in) &lt;br&gt;Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read"/>
    <param name="param_mascot_in" display="radio" type="boolean" truevalue="-mascot_in" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in mzData and write Mascot generic format" help="(-mascot_in) "/>
    <param name="param_mascot_out" display="radio" type="boolean" truevalue="-mascot_out" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in a Mascot results file (.mascotXML) and write idXML" help="(-mascot_out) "/>
    <param name="param_instrument" type="text" size="30" value="Default" label="the instrument that was used to measure the spectra" help="(-instrument) ">

    <data name="param_out" format="data"/>
  </outputs>
  <help>Annotates MS/MS spectra using Mascot.


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

7:fd960d61b64d

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

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

#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
]]></command>
  <inputs>
    <param name="param_in" type="data" format="txt" label="input file in mzData format" help="(-in) &lt;br&gt;Note: In mode 'mascot_out' a Mascot results file (.mascotXML) is read"/>
    <param name="param_mascot_in" display="radio" type="boolean" truevalue="-mascot_in" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in mzData and write Mascot generic format" help="(-mascot_in) "/>
    <param name="param_mascot_out" display="radio" type="boolean" truevalue="-mascot_out" falsevalue="" checked="false" optional="True" label="if this flag is set the MascotAdapter will read in a Mascot results file (.mascotXML) and write idXML" help="(-mascot_out) "/>
    <param name="param_instrument" type="text" size="30" value="Default" label="the instrument that was used to measure the spectra" help="(-instrument) ">

    <data name="param_out" format="data"/>
  </outputs>
  <help>Annotates MS/MS spectra using Mascot.


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