Mercurial > repos > jjohnson > spectrast2spectrast_irt

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/spectrast2spectrast_irt commit cf45d340518a13e8048c817aa8a61412c5e886db-dirty
author jjohnson
date Thu, 16 Aug 2018 10:30:02 -0400
parents f5ca880950f7
children
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1 <tool id="gp_spectrast2spectrast_irt" name="SpectraST RT Normalizer" version="0.5.0">
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2 <description></description>
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3 <requirements>
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4 <requirement type="package" version="0.5.0">msproteomicstools</requirement>
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5 </requirements>
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6 <stdio>
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7 <!-- Anything other than zero is an error -->
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8 <exit_code range="1:" />
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9 <exit_code range=":-1" />
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10 <!-- In case the return code has not been set propery check stderr too -->
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11 <regex match="Error:" />
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12 <regex match="Exception:" />
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13 </stdio>
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14 <command>
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15 <![CDATA[
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16 ## may have to link splib
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17 mkdir -p outdir &&
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18 spectrast2spectrast_irt.py
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19 --in ${input.extra_files_path}/library.sptxt
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20 --out outdir/library.splib
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21 #if i$kits.src == 'biognosys_irt':
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22 #if str($kits.kit) != 'None':
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23 --kit "#echo ",".join(str($kits.kit).split(','))#"
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24 #end if
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25 #elif $kits.src == 'history':
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26 #set $pep_irts = []
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27 #for line in open($kits.irt_file,'r').readlines():
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28 #silent $pep_irts.append(':'.join(line.strip().split('\t')))
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29 #end for
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30 --kit "#echo ",".join($pep_irts)#"
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31 #end if
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32 $applychauvenet
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33 $precursorlevel
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34 $spectralevel
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35 $report
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36 ##--exclude $exclude
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37 ##--surrogate $surrogate
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38 ##--linearregression $linearregression
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39 --rsq_threshold $rsq_threshold &&
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40 cp -p outdir/library.splib outdir/library.sptxt &&
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41 mkdir -p '$output.files_path' &&
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42 for i in library.splib library.sptxt library.spidx library.pepidx; do if [ -e outdir/\${i} ]; then cp -p outdir/\${i} '$output.files_path'; fi; done
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43 ]]>
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44 </command>
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45 <inputs>
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46 <param name="input" format="splib" type="data" label="Spectrast files" help="" />
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47
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48 <param name="applychauvenet" type="boolean" truevalue="--applychauvenet" falsevalue="" checked="False"
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49 label="Use Chavenet's criterion to exclude outliers" help="(--applychauvenet)" />
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50
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51 <param name="precursorlevel" type="boolean" truevalue="--precursorlevel" falsevalue="" checked="False"
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52 label="Use precursors instead of peptides for grouping" help="(--precursorlevel)" />
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53
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54 <param name="spectralevel" type="boolean" truevalue="--spectralevel" falsevalue="" checked="False"
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55 label="Do not merge or group any peptides or precursors" help="Use raw spectra. (--spectralevel)" />
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56
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57 <param name="report" type="boolean" truevalue="--report" falsevalue="" checked="False"
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58 label="Create a report CSV file" help="(--report)" />
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59
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60 <param name="rsq_threshold" type="float" value="0.95" label="Specify r-squared threshold to accept linear regression" help="(--rsq_threshold)" />
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61
2
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62 <conditional name="kits">
3
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63 <param name="src" type="select" label="iRT kit selection">
2
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64 <option value="biognosys_irt">Biognosys iRT</option>
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65 <option value="history">History dataset (2 columns: peptide iRT)</option>
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66 </param>
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67 <when value="biognosys_irt">
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68 <param name="kit" type="select" multiple="True" optional="True" label="Specifiy RT-kit">
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69 <option value="LGGNEQVTR:-28.3083">LGGNEQVTR:-28.3083</option>
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70 <option value="GAGSSEPVTGLDAK:0.227424">GAGSSEPVTGLDAK:0.227424</option>
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71 <option value="VEATFGVDESNAK:13.1078">VEATFGVDESNAK:13.1078</option>
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72 <option value="YILAGVENSK:22.3798">YILAGVENSK:22.3798</option>
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73 <option value="TPVISGGPYEYR:28.9999">TPVISGGPYEYR:28.9999</option>
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74 <option value="TPVITGAPYEYR:33.6311">TPVITGAPYEYR:33.6311</option>
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75 <option value="DGLDAASYYAPVR:43.2819">DGLDAASYYAPVR:43.2819</option>
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76 <option value="ADVTPADFSEWSK:54.969">ADVTPADFSEWSK:54.969</option>
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77 <option value="GTFIIDPGGVIR:71.3819">GTFIIDPGGVIR:71.3819</option>
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78 <option value="GTFIIDPAAVIR:86.7152">GTFIIDPAAVIR:86.7152</option>
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79 <option value="LFLQFGAQGSPFLK:98.0897">LFLQFGAQGSPFLK:98.0897</option>
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80 </param>
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81 </when>
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82 <when value="history">
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83 <param name="irt_file" type="data" format="tabular" label="Peptide iRT table"
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84 help="2 columns: peptide iRT" />
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85 </when>
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86 </conditional>
0
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87 </inputs>
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88 <outputs>
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89 <data name="output_report" format="csv" from_work_dir="outdir/library.csv">
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90 <filter>report</filter>
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91 </data>
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92 <data name="output" format="splib"/>
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93 </outputs>
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94 <tests>
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95 <!--
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96 <test>
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97 <param name="input" value="HEK_Lib_7Nov13.splib" ftype="txt" />
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98 <param name="report" value="True" />
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99 <output name="output_splib" file="spectrast2spectrast_irt_output_1_splib.txt" ftype="txt" />
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100 <output name="output_pepidx" file="spectrast2spectrast_irt_output_1_pepids.txt" ftype="txt" />
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101 <output name="output_report" file="spectrast2spectrast_irt_output_1_report.txt" ftype="txt" />
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102 </test>
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103 <test>
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104 <param name="input" value="HEK_Lib_7Nov13.splib" ftype="txt" />
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105 <param name="report" value="False" />
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106 <param name="kit" value="LGGNEQVTR:-28.3083,GAGSSEPVTGLDAK:0.227424" />
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107 <output name="output_splib" file="spectrast2spectrast_irt_output_2_splib.txt" ftype="txt" />
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108 <output name="output_pepidx" file="spectrast2spectrast_irt_output_2_pepids.txt" ftype="txt" />
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109 </test>
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110 -->
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111 </tests>
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112 <help>
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113 <![CDATA[
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114 **What it does**
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115
2
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116 SpectraST RT Normalizer
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117 ---------------------------------------------------------------------------------------------
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118 Usage: spectrast2spectrast_irt.py -i non_consensus_library.[splib/sptxt] -o non_consensus_library_irt.splib
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119 Input: SpectraST non_consensus_library.splib in txt format
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120 Output: SpectraST non_consensus_library_irt.[splib/pepidx] and regression plots for all runs.
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121 Argument: -i [--in]: input file
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122 -o [--out]: output file
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123 (optional) -k [--kit]: specifiy RT-kit [LGGNEQVTR:-28.3083,GAGSSEPVTGLDAK:0.227424,VEATFGVDESNAK:13.1078,YILAGVENSK:22.3798,TPVISGGPYEYR:28.9999,TPVITGAPYEYR:33.6311,DGLDAASYYAPVR:43.2819,ADVTPADFSEWSK:54.969,GTFIIDPGGVIR:71.3819,GTFIIDPAAVIR:86.7152,LFLQFGAQGSPFLK:98.0897]
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124 (optional) -a [--applychauvenet]: should Chavenet's criterion be used to exclude outliers?
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125 (optional) -p [--precursorlevel]: should precursors instead of peptides be used for grouping?
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126 (optional) [--spectralevel]: do not merge or group any peptides or precursors (use raw spectra)
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127 (optional) -r [--report]: should a csv report be written?
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128 (optional) -e [--exclude]: specify peptides from the RT-kit to exclude [run_id1:LGGNEQVTR,run_id2:GAGSSEPVTGLDAK]
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129 (optional) -s [--surrogate]: specify surrogate calibrations [broken_run_id1:working_run_id2]
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130 (optional) -l [--linearregression]: specify surrogate linear regressions (first number: c, second number: m) [broken_run_id1:1/3]
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131 (optional) -t [--rsq_threshold]: specify r-squared threshold to accept linear regression [0.95]
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132 Important: The splib need to be in txt format!
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133 spectrast -c_BIN! -cNnon_consensus.txt non_consensus.bin.splib
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134 All runs in your library further need to contain the Biognosys RT-kit peptides.
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135 Contact: George Rosenberger <rosenberger@imsb.biol.ethz.ch>
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136
0
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137
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138
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139 ]]>
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140 </help>
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141 <citations>
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142 </citations>
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143 </tool>