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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="MassCalculator" name="MassCalculator" version="1.12.0">
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3 <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">MassCalculator</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>MassCalculator
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11
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12 -in ${param_in}
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13 -in_seq ${param_in_seq}
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14 -out ${param_out}
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15 -charge ${param_charge}
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16 -format ${param_format}
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17 ${param_average_mass}
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18 -fragment_type ${param_fragment_type}
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19 -separator ${param_separator}
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20 -threads \${GALAXY_SLOTS:-24}
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21 </command>
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22 <inputs>
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23 <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)"/>
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24 <param name="param_in_seq" type="text" size="20" label="List of peptide sequences (mutually exclusive to 'in')" help="(-in_seq)"/>
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25 <param name="param_charge" type="text" size="20" value="0" label="List of charge states; required if 'in_seq' is given" help="(-charge)"/>
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26 <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)">
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27 <option value="list">list</option>
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28 <option value="table">table</option>
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29 <option value="mass_only">mass_only</option>
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30 <option value="mz_only">mz_only</option>
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31 </param>
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32 <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)"/>
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33 <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)">
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34 <option value="full">full</option>
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35 <option value="internal">internal</option>
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36 <option value="N-terminal">N-terminal</option>
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37 <option value="C-terminal">C-terminal</option>
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38 <option value="a-ion">a-ion</option>
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39 <option value="b-ion">b-ion</option>
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40 <option value="c-ion">c-ion</option>
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41 <option value="x-ion">x-ion</option>
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42 <option value="y-ion">y-ion</option>
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43 <option value="z-ion">z-ion</option>
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44 </param>
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45 <param name="param_separator" type="text" size="20" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="(-separator)"/>
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46 </inputs>
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47 <outputs>
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48 <data name="param_out" label="Output file; if empty, output is written to the screen" format="txt"/>
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49 </outputs>
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50 <help>**What it does**
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51
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52 Calculates masses and mass-to-charge ratios of peptide sequences
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53
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54
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55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MassCalculator.html
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56
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57 @REFERENCES@
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58 </help>
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59 </tool>
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