annotate delta_pi_calc.xml @ 3:78afc81ab244 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit decb06dc90d7069d317968b979f649a04720b264
author galaxyp
date Thu, 14 Sep 2017 11:55:02 -0400
parents 77ddaee887a8
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78afc81ab244 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit decb06dc90d7069d317968b979f649a04720b264
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1 <tool id="calc_delta_pi" name="Add delta pI" version="1.3">
2
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2 <description>to peptide table</description>
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3 <requirements>
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4 <requirement type="package" version="3.6">python</requirement>
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5 </requirements>
2
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6 <command detect_errors="exit_code">
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7 python '$__tool_directory__/peptide_pi_annotator.py' -i '$trainingpi' -p '$peptable' --out '$output'
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8 #if $stripcol
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9 --stripcol $stripcol
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10 #else if $stripcolpattern
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11 --stripcolpattern '$stripcolpattern'
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12 #end if
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13 #if $pepcol
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14 --pepcol $pepcol
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15 #else if $pepcolpattern
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16 --pepcolpattern '$pepcolpattern'
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17 #end if
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18 #if $fraccol
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19 --fraccol $fraccol
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20 #else if $fraccolpattern
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21 --fraccolpattern '$fraccolpattern'
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22 #end if
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24 --strippatterns
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25 #for $strip in $strips
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26 '$strip.pattern'
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27 #end for
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28
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29 --intercepts
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30 #for $strip in $strips
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31 $strip.intercept
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32 #end for
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33
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34 --widths
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35 #for $strip in $strips
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36 $strip.fr_width
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37 #end for
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38
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39 #if len($ignoremods) > 0
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40 --ignoremods
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41 #for $mod in $ignoremods
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42 '$mod.regex'
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43 #end for
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44 #end if
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45 </command>
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46
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47 <inputs>
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48 <param name="trainingpi" type="data" format="tabular" label="Known peptides with annotation of pI" help="First column is sequence, second pI" />
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49 <param name="peptable" type="data" format="tabular" label="Peptide table to determine pI shift from" />
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50 <repeat name="ignoremods" title="Peptide modification weights to ignore">
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51 <param name="regex" label="Regex to strip modification from peptide table before looking up sequence in predicted pI" type="text" help="Enter e.g. 15.994915 for oxidation, * to ignore all modifications, or a proper regex (however brackets are stripped by galaxy). See help below.">
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52 <sanitizer>
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53 <valid>
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54 <remove preset="string.whitespace" />
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55 </valid>
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56 </sanitizer>
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57 </param>
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58 </repeat>
1
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59 <param name="pepcolpattern" type="text" value="" optional="true" label="Peptide sequence pattern for column header field in peptide table." />
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60 <param name="pepcol" type="integer" value="" optional="true" label="Peptide sequence column number in peptide table. First column is 1. Overrides column pattern." />
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61 <param name="fraccolpattern" type="text" value="" optional="true" label="Fraction number column header papttern in peptide table." />
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62 <param name="fraccol" type="integer" optional="true" value="" label="Fraction number column number in peptide table. First column is 1. Overrides column pattern." />
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63 <param name="stripcolpattern" type="text" optional="true" value="" label="Strip pattern header column pattern in peptide table" help="E.g. column with filename to derive strip name from"/>
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64 <param name="stripcol" type="integer" optional="true" value="" label="Strip pattern column number in peptide table" help="E.g. column with filename to derive strip name from. First column is 1. Overrides column pattern"/>
0
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65 <repeat name="strips" title="pI separation strip data">
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66 <param name="pattern" type="text" label="Strip regex detection pattern" help="Regex (see help below) that identifies the pI strip from the column in the above field.">
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67 <sanitizer>
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68 <valid>
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69 <remove preset="string.whitespace" />
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70 </valid>
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71 </sanitizer>
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72 </param>
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73 <param name="intercept" type="text" label="pI intercept of strip" />
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74 <param name="fr_width" type="text" label="fraction widths" />
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75 </repeat>
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76 </inputs>
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77
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78 <outputs>
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79 <data format="tabular" name="output"/>
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80 </outputs>
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81 <tests>
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82 <test>
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83 <param name="trainingpi" value="predicted_peptides.txt" />
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84 <param name="peptable" value="peptable.txt" />
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85 <repeat name="ignoremods">
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86 <param name="regex" value="*" />
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87 </repeat>
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88 <param name="pepcol" value="1" />
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89 <param name="fraccol" value="4" />
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90 <param name="stripcol" value="2" />
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galaxyp
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91 <repeat name="strips">
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92 <param name="pattern" value="strip1" />
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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93 <param name="intercept" value="8.21" />
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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94 <param name="fr_width" value="0.013" />
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95 </repeat>
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
galaxyp
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96 <repeat name="strips">
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97 <param name="pattern" value="strip2" />
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98 <param name="intercept" value="6.11" />
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99 <param name="fr_width" value="0.04" />
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100 </repeat>
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101 <output name="output" value="peptable_deltapi.txt" />
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102 </test>
1
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103 <test>
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104 <param name="trainingpi" value="predicted_peptides.txt" />
8a30d6e5b97d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit ddcc42d2a767f7c14eb710b8ac264745c25444d3
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105 <param name="peptable" value="peptable.txt" />
8a30d6e5b97d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit ddcc42d2a767f7c14eb710b8ac264745c25444d3
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106 <repeat name="ignoremods">
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107 <param name="regex" value="*" />
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108 </repeat>
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109 <param name="pepcolpattern" value="Sequence" />
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110 <param name="fraccolpattern" value="Fraction" />
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111 <param name="stripcolpattern" value="Filename" />
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112 <repeat name="strips">
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113 <param name="pattern" value="strip1" />
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114 <param name="intercept" value="8.21" />
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115 <param name="fr_width" value="0.013" />
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116 </repeat>
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117 <repeat name="strips">
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118 <param name="pattern" value="strip2" />
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119 <param name="intercept" value="6.11" />
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120 <param name="fr_width" value="0.04" />
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121 </repeat>
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122 <output name="output" value="peptable_deltapi.txt" />
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123 </test>
0
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124 <test>
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125 <param name="trainingpi" value="predicted_peptides.txt" />
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126 <param name="peptable" value="peptable.txt" />
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127 <repeat name="ignoremods">
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128 <param name="regex" value="15.994915" />
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129 </repeat>
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130 <param name="pepcol" value="1" />
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131 <param name="fraccol" value="4" />
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132 <param name="stripcol" value="2" />
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133 <repeat name="strips">
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134 <param name="pattern" value="strip1" />
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135 <param name="intercept" value="8.21" />
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136 <param name="fr_width" value="0.013" />
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137 </repeat>
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138 <repeat name="strips">
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139 <param name="pattern" value="strip2" />
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140 <param name="intercept" value="6.11" />
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141 <param name="fr_width" value="0.04" />
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142 </repeat>
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143 <output name="output" value="peptable_deltapi.txt" />
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144 </test>
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145 <test>
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146 <param name="trainingpi" value="predicted_peptides.txt" />
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147 <param name="peptable" value="peptable.txt" />
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148 <param name="pepcol" value="1" />
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149 <param name="fraccol" value="4" />
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150 <param name="stripcol" value="2" />
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151 <repeat name="strips">
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152 <param name="pattern" value="strip1" />
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153 <param name="intercept" value="8.21" />
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154 <param name="fr_width" value="0.013" />
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155 </repeat>
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156 <repeat name="strips">
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157 <param name="pattern" value="strip2" />
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158 <param name="intercept" value="6.11" />
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159 <param name="fr_width" value="0.04" />
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160 </repeat>
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161 <output name="output" value="peptable_missed_ox.txt" />
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162 </test>
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163 </tests>
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164
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165 <help>
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166 In case you have no pI calculation method but a large table with
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167 peptides and their predicted pIs available. This tool adds a column
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168 with delta-pI values to a peptide or PSM table for each peptide it
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169 can find in the predicted collection. Needs a tab-separated file
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170 with peptide-sequences and their predicted pI, and a PSM/peptide table
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171 with at least peptide sequences.
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172
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173 Regexes, or regular expressions are are sequences of characters that
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174 are used to find a certain pattern in a string of text. For example
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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175 the regex "peptide" will find the word "peptide" in the text
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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176 "thisisa peptide in my sample". More advanced regexes can allow for
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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177 finding for example specific but variable pieces of text, e.g.
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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178 "[a-c].*" will match a string "acbcba" in "yxyzyxacbcbayxzyxyzxy".
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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179 Much more elaborate regexes exist. Since this is a python script,
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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180 python regexes are described here:
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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181 https://docs.python.org/3/library/re.html
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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182 </help>
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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183
34c5c95740a1 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit a58e2a324724f344a07d4499c860a5b2da06927d
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184 </tool>