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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="AdditiveSeries" name="AdditiveSeries" version="2.0.0">
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3 <description>Computes an additive series to quantify a peptide in a set of samples.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">AdditiveSeries</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>AdditiveSeries
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11
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12 -in
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13 #for token in $param_in:
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14 $token
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15 #end for
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16 #if $param_out:
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17 -out $param_out
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18 #end if
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19 #if $param_mz_tolerance:
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20 -mz_tolerance $param_mz_tolerance
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21 #end if
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22 #if $param_rt_tolerance:
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23 -rt_tolerance $param_rt_tolerance
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24 #end if
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25
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26 #if $rep_param_concentrations:
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27 -concentrations
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28 #for token in $rep_param_concentrations:
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29 #if " " in str(token):
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30 "$token.param_concentrations"
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31 #else
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32 $token.param_concentrations
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33 #end if
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34 #end for
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35 #end if
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36 #if $param_feature_rt:
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37 -feature_rt $param_feature_rt
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38 #end if
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39 #if $param_feature_mz:
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40 -feature_mz $param_feature_mz
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41 #end if
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42 #if $param_standard_rt:
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43 -standard_rt $param_standard_rt
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44 #end if
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45 #if $param_standard_mz:
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46 -standard_mz $param_standard_mz
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47 #end if
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48 -threads \${GALAXY_SLOTS:-24}
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49 #if $param_plot_write_gnuplot_output:
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50 -plot:write_gnuplot_output
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51 #end if
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52 #if $param_plot_out_gp:
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53 -plot:out_gp "$param_plot_out_gp"
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54 #end if
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55 #if $adv_opts.adv_opts_selector=='advanced':
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56 #if $adv_opts.param_force:
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57 -force
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58 #end if
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59 #end if
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60 </command>
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61 <inputs>
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62 <param name="param_in" type="data" format="featurexml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) ">
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63 <sanitizer>
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64 <valid initial="string.printable">
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65 <remove value="'"/>
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66 <remove value="""/>
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67 </valid>
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68 </sanitizer>
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69 </param>
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70 <param name="param_mz_tolerance" type="float" value="1.0" label="Tolerance in m/z dimension" help="(-mz_tolerance) "/>
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71 <param name="param_rt_tolerance" type="float" value="1.0" label="Tolerance in RT dimension" help="(-rt_tolerance) "/>
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72 <repeat name="rep_param_concentrations" min="1" title="param_concentrations">
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73 <param name="param_concentrations" type="text" size="30" value="0" label="List of spiked concentrations" help="(-concentrations) ">
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74 <sanitizer>
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75 <valid initial="string.printable">
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76 <remove value="'"/>
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77 <remove value="""/>
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78 </valid>
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79 </sanitizer>
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80 </param>
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81 </repeat>
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82 <param name="param_feature_rt" type="float" value="-1.0" label="RT position of the feature" help="(-feature_rt) "/>
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83 <param name="param_feature_mz" type="float" value="-1.0" label="m/z position of the feature" help="(-feature_mz) "/>
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84 <param name="param_standard_rt" type="float" value="-1.0" label="RT position of the standard" help="(-standard_rt) "/>
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85 <param name="param_standard_mz" type="float" value="-1.0" label="m/z position of the standard" help="(-standard_mz) "/>
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86 <param name="param_plot_write_gnuplot_output" type="boolean" truevalue="-plot:write_gnuplot_output" falsevalue="" checked="false" optional="True" label="Flag that activates the GNUplot output" help="(-write_gnuplot_output) "/>
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87 <param name="param_plot_out_gp" type="text" size="30" label="base file name (3 files with different extensions are created)" help="(-out_gp) ">
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88 <sanitizer>
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89 <valid initial="string.printable">
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90 <remove value="'"/>
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91 <remove value="""/>
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92 </valid>
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93 </sanitizer>
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94 </param>
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95 <expand macro="advanced_options">
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96 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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97 </expand>
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98 </inputs>
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99 <outputs>
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100 <data name="param_out" format="xml"/>
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101 </outputs>
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102 <help>**What it does**
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103
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104 Computes an additive series to quantify a peptide in a set of samples.
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105
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106
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107 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_AdditiveSeries.html</help>
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108 <expand macro="references"/>
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109 </tool>
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