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annotate ProteinQuantifier.xml @ 4:6ead64a594bd draft default tip

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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4
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1 <?xml version="1.0" encoding="UTF-8"?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Quantitation]-->
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4 <tool id="ProteinQuantifier" name="ProteinQuantifier" version="2.0.0">
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5 <description>Compute peptide and protein abundances</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">ProteinQuantifier</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>ProteinQuantifier
0
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14
4
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_protein_groups:
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19 -protein_groups $param_protein_groups
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20 #end if
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21 #if $param_out:
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22 -out $param_out
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23 #end if
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24 #if $param_peptide_out:
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25 -peptide_out $param_peptide_out
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26 #end if
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27 #if $param_top:
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28 -top $param_top
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29 #end if
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30 #if $param_average:
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31 -average
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32 #if &quot; &quot; in str($param_average):
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33 &quot;$param_average&quot;
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34 #else
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35 $param_average
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36 #end if
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37 #end if
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38 #if $param_include_all:
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39 -include_all
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40 #end if
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41 #if $param_filter_charge:
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42 -filter_charge
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43 #end if
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44 #if $param_ratios:
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45 -ratios
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46 #end if
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47 #if $param_ratiosSILAC:
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48 -ratiosSILAC
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49 #end if
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50 -threads \${GALAXY_SLOTS:-24}
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51 #if $param_consensus_normalize:
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52 -consensus:normalize
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53 #end if
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54 #if $param_consensus_fix_peptides:
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55 -consensus:fix_peptides
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56 #end if
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57 #if $param_format_separator:
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58 -format:separator &quot;$param_format_separator&quot;
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59 #end if
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60 #if $param_format_quoting:
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61 -format:quoting
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62 #if &quot; &quot; in str($param_format_quoting):
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63 &quot;$param_format_quoting&quot;
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64 #else
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65 $param_format_quoting
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66 #end if
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67 #end if
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68 #if $param_format_replacement:
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69 -format:replacement &quot;$param_format_replacement&quot;
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70 #end if
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71 #if $adv_opts.adv_opts_selector=='advanced':
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72 #if $adv_opts.param_force:
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73 -force
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74 #end if
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75 #end if
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76 </command>
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77 <inputs>
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78 <param format="xml,consensusxml" help="(-in) " label="Input file" name="param_in" optional="False" type="data"/>
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79 <param format="xml" help="(-protein_groups) e.g. from ProteinProphet via IDFileConverter or Fido via FidoAdapter). &lt;br&gt;Information about indistinguishable proteins will be used for protein quantification" label="Protein inference results for the identification runs that were used to annotate the input (" name="param_protein_groups" optional="True" type="data"/>
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80 <param help="(-top) " label="Calculate protein abundance from this number of proteotypic peptides (most abundant first; '0' for all)" min="0" name="param_top" optional="True" type="integer" value="3"/>
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81 <param help="(-average) " label="Averaging method used to compute protein abundances from peptide abundances" name="param_average" optional="True" type="select" value="median">
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82 <option value="median">median</option>
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83 <option value="mean">mean</option>
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84 <option value="weighted_mean">weighted_mean</option>
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85 <option value="sum">sum</option>
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86 </param>
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87 <param checked="false" falsevalue="" help="(-include_all) " label="Include results for proteins with fewer proteotypic peptides than indicated by 'top' (no effect if 'top' is 0 or 1)" name="param_include_all" optional="True" truevalue="-include_all" type="boolean"/>
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88 <param checked="false" falsevalue="" help="(-filter_charge) For peptides, abundances will be reported separately for each charge; &lt;br&gt;for proteins, abundances will be computed based only on the most prevalent charge of each peptide. &lt;br&gt;By default, abundances are summed over all charge states" label="Distinguish between charge states of a peptide" name="param_filter_charge" optional="True" truevalue="-filter_charge" type="boolean"/>
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89 <param checked="false" falsevalue="" help="(-ratios) Format: log_2(x_0/x_0) &lt;sep&gt; log_2(x_1/x_0) &lt;sep&gt; log_2(x_2/x_0) " label="Add the log2 ratios of the abundance values to the output" name="param_ratios" optional="True" truevalue="-ratios" type="boolean"/>
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90 <param checked="false" falsevalue="" help="(-ratiosSILAC) Only applicable to consensus maps of exactly three sub-maps. Format: log_2(heavy/light) &lt;sep&gt; log_2(heavy/middle) &lt;sep&gt; log_2(middle/light)" label="Add the log2 ratios for a triple SILAC experiment to the output" name="param_ratiosSILAC" optional="True" truevalue="-ratiosSILAC" type="boolean"/>
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91 <param checked="false" falsevalue="" help="(-normalize) " label="Scale peptide abundances so that medians of all samples are equal" name="param_consensus_normalize" optional="True" truevalue="-consensus:normalize" type="boolean"/>
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92 <param checked="false" falsevalue="" help="(-fix_peptides) &lt;br&gt;With 'top 0', all peptides that occur in every sample are considered. &lt;br&gt;Otherwise ('top N'), the N peptides that occur in the most samples (independently of each other) are selected, &lt;br&gt;breaking ties by total abundance (there is no guarantee that the best co-ocurring peptides are chosen!)" label="Use the same peptides for protein quantification across all samples" name="param_consensus_fix_peptides" optional="True" truevalue="-consensus:fix_peptides" type="boolean"/>
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93 <param help="(-separator) " label="Character(s) used to separate fields; by default, the 'tab' character is used" name="param_format_separator" size="30" type="text">
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94 <sanitizer>
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95 <valid initial="string.printable">
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96 <remove value="'"/>
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97 <remove value="&quot;"/>
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98 </valid>
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99 </sanitizer>
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100 </param>
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101 <param help="(-quoting) " label="Method for quoting of strings: 'none' for no quoting, 'double' for quoting with doubling of embedded quotes, &lt;br&gt;'escape' for quoting with backslash-escaping of embedded quotes" name="param_format_quoting" optional="True" type="select" value="double">
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102 <option value="none">none</option>
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103 <option value="double">double</option>
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104 <option value="escape">escape</option>
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105 </param>
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106 <param help="(-replacement) " label="If 'quoting' is 'none', used to replace occurrences of the separator in strings before writing" name="param_format_replacement" size="30" type="text" value="_">
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107 <sanitizer>
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108 <valid initial="string.printable">
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109 <remove value="'"/>
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110 <remove value="&quot;"/>
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111 </valid>
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112 </sanitizer>
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113 </param>
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114 <expand macro="advanced_options">
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115 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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116 </expand>
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117 </inputs>
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118 <outputs>
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119 <data format="tabular" name="param_out"/>
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120 <data format="tabular" name="param_peptide_out"/>
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121 </outputs>
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122 <help>Compute peptide and protein abundances
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123
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124
4
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125 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_ProteinQuantifier.html</help>
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126 </tool>