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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="ProteinQuantifier" name="ProteinQuantifier" version="2.0.0">
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3 <description>Compute peptide and protein abundances</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">ProteinQuantifier</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>ProteinQuantifier
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11
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12 #if $param_in:
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13 -in $param_in
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14 #end if
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15 #if $param_protein_groups:
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16 -protein_groups $param_protein_groups
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_peptide_out:
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22 -peptide_out $param_peptide_out
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23 #end if
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24 #if $param_top:
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25 -top $param_top
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26 #end if
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27 #if $param_average:
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28 -average
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29 #if " " in str($param_average):
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30 "$param_average"
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31 #else
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32 $param_average
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33 #end if
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34 #end if
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35 #if $param_include_all:
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36 -include_all
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37 #end if
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38 #if $param_filter_charge:
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39 -filter_charge
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40 #end if
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41 #if $param_ratios:
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42 -ratios
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43 #end if
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44 #if $param_ratiosSILAC:
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45 -ratiosSILAC
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46 #end if
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47 -threads \${GALAXY_SLOTS:-24}
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48 #if $param_consensus_normalize:
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49 -consensus:normalize
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50 #end if
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51 #if $param_consensus_fix_peptides:
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52 -consensus:fix_peptides
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53 #end if
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54 #if $param_format_separator:
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55 -format:separator "$param_format_separator"
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56 #end if
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57 #if $param_format_quoting:
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58 -format:quoting
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59 #if " " in str($param_format_quoting):
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60 "$param_format_quoting"
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61 #else
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62 $param_format_quoting
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63 #end if
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64 #end if
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65 #if $param_format_replacement:
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66 -format:replacement "$param_format_replacement"
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67 #end if
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68 #if $adv_opts.adv_opts_selector=='advanced':
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69 #if $adv_opts.param_force:
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70 -force
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71 #end if
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72 #end if
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73 </command>
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74 <inputs>
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75 <param name="param_in" type="data" format="featurexml,consensusxml,idxml" optional="False" label="Input file" help="(-in) "/>
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76 <param name="param_protein_groups" type="data" format="idxml" optional="True" label="Protein inference results for the identification runs that were used to annotate the input (" help="(-protein_groups) e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter). <br>Information about indistinguishable proteins will be used for protein quantification"/>
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77 <param name="param_top" type="integer" min="0" optional="True" value="3" label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" help="(-top) "/>
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78 <param name="param_average" type="select" optional="True" value="median" label="Averaging method used to compute protein abundances from peptide abundances" help="(-average) ">
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79 <option value="median">median</option>
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80 <option value="mean">mean</option>
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81 <option value="weighted_mean">weighted_mean</option>
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82 <option value="sum">sum</option>
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83 </param>
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84 <param name="param_include_all" type="boolean" truevalue="-include_all" falsevalue="" checked="false" optional="True" label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" help="(-include_all) "/>
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85 <param name="param_filter_charge" type="boolean" truevalue="-filter_charge" falsevalue="" checked="false" optional="True" label="Distinguish between charge states of a peptide" help="(-filter_charge) For peptides, abundances will be reported separately for each charge; <br>for proteins, abundances will be computed based only on the most prevalent charge of each peptide. <br>By default, abundances are summed over all charge states"/>
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86 <param name="param_ratios" type="boolean" truevalue="-ratios" falsevalue="" checked="false" optional="True" label="Add the log2 ratios of the abundance values to the output" help="(-ratios) Format: log_2(x_0/x_0) <sep> log_2(x_1/x_0) <sep> log_2(x_2/x_0) "/>
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87 <param name="param_ratiosSILAC" type="boolean" truevalue="-ratiosSILAC" falsevalue="" checked="false" optional="True" label="Add the log2 ratios for a triple SILAC experiment to the output" help="(-ratiosSILAC) Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) <sep> log_2(heavy/middle) <sep> log_2(middle/light)"/>
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88 <param name="param_consensus_normalize" type="boolean" truevalue="-consensus:normalize" falsevalue="" checked="false" optional="True" label="Scale peptide abundances so that medians of all samples are equal" help="(-normalize) "/>
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89 <param name="param_consensus_fix_peptides" type="boolean" truevalue="-consensus:fix_peptides" falsevalue="" checked="false" optional="True" label="Use the same peptides for protein quantification across all samples" help="(-fix_peptides) <br>With 'top 0', all peptides that occur in every sample are considered. <br>Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected, <br>breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)"/>
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90 <param name="param_format_separator" type="text" size="30" label="Character(s) used to separate fields; by default, the 'tab' character is used" help="(-separator) ">
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91 <sanitizer>
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92 <valid initial="string.printable">
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93 <remove value="'"/>
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94 <remove value="""/>
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95 </valid>
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96 </sanitizer>
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97 </param>
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98 <param name="param_format_quoting" type="select" optional="True" value="double" label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes, <br>'escape' for quoting with backslash-escaping of embedded quotes" help="(-quoting) ">
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99 <option value="none">none</option>
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100 <option value="double">double</option>
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101 <option value="escape">escape</option>
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102 </param>
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103 <param name="param_format_replacement" type="text" size="30" value="_" label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" help="(-replacement) ">
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104 <sanitizer>
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105 <valid initial="string.printable">
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106 <remove value="'"/>
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107 <remove value="""/>
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108 </valid>
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109 </sanitizer>
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110 </param>
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111 <expand macro="advanced_options">
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112 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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113 </expand>
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114 </inputs>
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115 <outputs>
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116 <data name="param_out" format="tabular"/>
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117 <data name="param_peptide_out" format="tabular"/>
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118 </outputs>
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119 <help>**What it does**
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120
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121 Compute peptide and protein abundances
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122
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123
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124 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinQuantifier.html</help>
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125 <expand macro="references"/>
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126 </tool>
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