comparison MassCalculator.xml @ 4:6ead64a594bd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty

3:ec62782f6c68

<?xml version='1.0' encoding='UTF-8'?>
<tool id="MassCalculator" name="MassCalculator" version="1.12.0">
  <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
  <macros>
    <token name="@EXECUTABLE@">MassCalculator</token>
    <import>macros.xml</import>
  </macros>
  <expand macro="stdio"/>
  <expand macro="requirements"/>
  <command>MassCalculator

-in ${param_in}
-in_seq ${param_in_seq}
-out ${param_out}
-charge ${param_charge}
-format ${param_format}
${param_average_mass}
-fragment_type ${param_fragment_type}
-separator ${param_separator}
-threads \${GALAXY_SLOTS:-24} 
</command>
  <inputs>
    <param name="param_in" type="data" format="txt" optional="True" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help="(-in)"/>
    <param name="param_in_seq" type="text" size="20" label="List of peptide sequences (mutually exclusive to 'in')" help="(-in_seq)"/>
    <param name="param_charge" type="text" size="20" value="0" label="List of charge states; required if 'in_seq' is given" help="(-charge)"/>
    <param name="param_format" type="select" optional="True" value="list" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)#br#" help="(-format)">
      <option value="list">list</option>
      <option value="table">table</option>
      <option value="mass_only">mass_only</option>
      <option value="mz_only">mz_only</option>
    </param>
    <param name="param_average_mass" type="boolean" truevalue="-average_mass true" falsevalue="-average_mass false" checked="false" optional="True" label="Compute average (instead of monoisotopic) peptide masses" help="(-average_mass)"/>
    <param name="param_fragment_type" type="select" optional="True" value="full" label="For what type of sequence/fragment the mass should be computed#br#" help="(-fragment_type)">
      <option value="full">full</option>
      <option value="internal">internal</option>
      <option value="N-terminal">N-terminal</option>
      <option value="C-terminal">C-terminal</option>
      <option value="a-ion">a-ion</option>
      <option value="b-ion">b-ion</option>
      <option value="c-ion">c-ion</option>
      <option value="x-ion">x-ion</option>
      <option value="y-ion">y-ion</option>
      <option value="z-ion">z-ion</option>
    </param>
    <param name="param_separator" type="text" size="20" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="(-separator)"/>
  </inputs>
  <outputs>
    <data name="param_out" label="Output file; if empty, output is written to the screen" format="txt"/>
  </outputs>
  <help>**What it does**

Calculates masses and mass-to-charge ratios of peptide sequences


For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MassCalculator.html

@REFERENCES@
</help>
</tool>

4:6ead64a594bd

<?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: [Utilities]-->
  <tool id="MassCalculator" name="MassCalculator" version="2.0.0">
    <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
    <macros>
      <token name="@EXECUTABLE@">MassCalculator</token>
      <import>macros.xml</import>
    </macros>
    <expand macro="references"/>
    <expand macro="stdio"/>
    <expand macro="requirements"/>
    <command>MassCalculator

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

#if $rep_param_in_seq:
-in_seq
  #for token in $rep_param_in_seq:
    #if &quot; &quot; in str(token):
      &quot;$token.param_in_seq&quot;
    #else
      $token.param_in_seq
    #end if
  #end for
#end if
#if $param_out:
  -out $param_out
#end if

#if $rep_param_charge:
-charge
  #for token in $rep_param_charge:
    #if &quot; &quot; in str(token):
      &quot;$token.param_charge&quot;
    #else
      $token.param_charge
    #end if
  #end for
#end if
#if $param_format:
  -format
  #if &quot; &quot; in str($param_format):
    &quot;$param_format&quot;
  #else
    $param_format
  #end if
#end if
#if $param_average_mass:
  -average_mass
#end if
#if $param_fragment_type:
  -fragment_type
  #if &quot; &quot; in str($param_fragment_type):
    &quot;$param_fragment_type&quot;
  #else
    $param_fragment_type
  #end if
#end if
#if $param_separator:
  -separator     &quot;$param_separator&quot;
#end if
-threads \${GALAXY_SLOTS:-24}
#if $adv_opts.adv_opts_selector=='advanced':
    #if $adv_opts.param_force:
  -force
#end if
#end if
</command>
    <inputs>
      <param format="txt" help="(-in) " label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" name="param_in" optional="True" type="data"/>
      <repeat min="0" name="rep_param_in_seq" title="param_in_seq">
        <param help="(-in_seq) " label="List of peptide sequences (mutually exclusive to 'in')" name="param_in_seq" size="30" type="text">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </repeat>
      <repeat max="1" min="0" name="rep_param_charge" title="param_charge">
        <param help="(-charge) " label="List of charge states; required if 'in_seq' is given" name="param_charge" size="30" type="text" value="0">
          <sanitizer>
            <valid initial="string.printable">
              <remove value="'"/>
              <remove value="&quot;"/>
            </valid>
          </sanitizer>
        </param>
      </repeat>
      <param help="(-format) " label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" name="param_format" optional="True" type="select" value="list">
        <option value="list">list</option>
        <option value="table">table</option>
        <option value="mass_only">mass_only</option>
        <option value="mz_only">mz_only</option>
      </param>
      <param checked="false" falsevalue="" help="(-average_mass) " label="Compute average (instead of monoisotopic) peptide masses" name="param_average_mass" optional="True" truevalue="-average_mass" type="boolean"/>
      <param help="(-fragment_type) " label="For what type of sequence/fragment the mass should be computed" name="param_fragment_type" optional="True" type="select" value="full">
        <option value="full">full</option>
        <option value="internal">internal</option>
        <option value="N-terminal">N-terminal</option>
        <option value="C-terminal">C-terminal</option>
        <option value="a-ion">a-ion</option>
        <option value="b-ion">b-ion</option>
        <option value="c-ion">c-ion</option>
        <option value="x-ion">x-ion</option>
        <option value="y-ion">y-ion</option>
        <option value="z-ion">z-ion</option>
      </param>
      <param help="(-separator) " label="Field separator for 'table' output format; by default, the 'tab' character is used" name="param_separator" size="30" type="text">
        <sanitizer>
          <valid initial="string.printable">
            <remove value="'"/>
            <remove value="&quot;"/>
          </valid>
        </sanitizer>
      </param>
      <expand macro="advanced_options">
        <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
      </expand>
    </inputs>
    <outputs>
      <data format="txt" name="param_out"/>
    </outputs>
    <help>Calculates masses and mass-to-charge ratios of peptide sequences


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