comparison InspectAdapter.xml @ 1:15ebe1509e0d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14

0:4fba18bcca36

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Identification]-->
<tool id="InspectAdapter" name="InspectAdapter" version="2.1.0">
  <description>Annotates MS/MS spectra using Inspect.</description>
  <macros>
    <token name="@EXECUTABLE@">InspectAdapter</token>
    <import>macros.xml</import>
  </macros>

  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzxml" optional="False" label="input file in mzXML or mzData format" help="(-in) &lt;br&gt;Note: In mode 'inspect_out' an Inspect results file is read"/>
    <param name="param_inspect_in" display="radio" type="boolean" truevalue="-inspect_in" falsevalue="" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in mzXML, &lt;br&gt;write an Inspect input file and generate a trie database" help="(-inspect_in) "/>
    <param name="param_inspect_out" display="radio" type="boolean" truevalue="-inspect_out" falsevalue="" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in a Inspect results file &lt;br&gt;and write idXML" help="(-inspect_out) "/>
    <param name="param_inspect_directory" type="text" size="30" label="the directory in which Inspect is located" help="(-inspect_directory) ">
      <sanitizer>
        <valid initial="string.printable">

          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_inspect_input" type="data" format="text" label="name for the input file of Inspect (may only be used in a full run)" help="(-inspect_input) "/>
    <param name="param_multicharge" display="radio" type="boolean" truevalue="-multicharge" falsevalue="" checked="false" optional="True" label="attempt to guess the precursor charge and mass, &lt;br&gt;and consider multiple charge states if feasible" help="(-multicharge) "/>
    <param name="param_max_modifications_pp" type="integer" value="-1" label="number of PTMs permitted in a single peptide" help="(-max_modifications_pp) "/>
    <param name="param_tag_count" type="integer" value="-1" label="number of tags to generate" help="(-tag_count) "/>
    <param name="param_no_tmp_dbs" display="radio" type="boolean" truevalue="-no_tmp_dbs" falsevalue="" checked="false" optional="True" label="no temporary databases are used" help="(-no_tmp_dbs) "/>
    <param name="param_p_value" type="float" value="1.0" label="annotations with inferior p-value are ignored" help="(-p_value) "/>

1:15ebe1509e0d

<?xml version='1.0' encoding='UTF-8'?>
<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
<!--Proposed Tool Section: [Identification]-->
<tool id="InspectAdapter" name="InspectAdapter" version="2.2.0.1">
  <description>Annotates MS/MS spectra using Inspect.</description>
  <macros>
    <token name="@EXECUTABLE@">InspectAdapter</token>
    <import>macros.xml</import>
  </macros>

  -force
#end if
#end if
</command>
  <inputs>
    <param name="param_in" type="data" format="mzxml,mzData" optional="False" label="input file in mzXML or mzData format" help="(-in) &lt;br&gt;Note: In mode 'inspect_out' an Inspect results file is read"/>
    <param name="param_inspect_in" display="radio" type="boolean" truevalue="-inspect_in" falsevalue="" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in mzXML, &lt;br&gt;write an Inspect input file and generate a trie database" help="(-inspect_in) "/>
    <param name="param_inspect_out" display="radio" type="boolean" truevalue="-inspect_out" falsevalue="" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in a Inspect results file &lt;br&gt;and write idXML" help="(-inspect_out) "/>
    <param name="param_inspect_directory" type="text" size="30" label="the directory in which Inspect is located" help="(-inspect_directory) ">
      <sanitizer>
        <valid initial="string.printable">

          <remove value="'"/>
          <remove value="&quot;"/>
        </valid>
      </sanitizer>
    </param>
    <param name="param_inspect_input" type="data" format="txt" label="name for the input file of Inspect (may only be used in a full run)" help="(-inspect_input) "/>
    <param name="param_multicharge" display="radio" type="boolean" truevalue="-multicharge" falsevalue="" checked="false" optional="True" label="attempt to guess the precursor charge and mass, &lt;br&gt;and consider multiple charge states if feasible" help="(-multicharge) "/>
    <param name="param_max_modifications_pp" type="integer" value="-1" label="number of PTMs permitted in a single peptide" help="(-max_modifications_pp) "/>
    <param name="param_tag_count" type="integer" value="-1" label="number of tags to generate" help="(-tag_count) "/>
    <param name="param_no_tmp_dbs" display="radio" type="boolean" truevalue="-no_tmp_dbs" falsevalue="" checked="false" optional="True" label="no temporary databases are used" help="(-no_tmp_dbs) "/>
    <param name="param_p_value" type="float" value="1.0" label="annotations with inferior p-value are ignored" help="(-p_value) "/>