Mercurial > repos > jay > pdaug_peptide_sequence_analysis
annotate PDAUG_Peptide_Sequence_Analysis/PDAUG_Peptide_Sequence_Analysis.xml @ 5:d11a54691a2f draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
author | jay |
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date | Thu, 28 Jan 2021 02:41:47 +0000 |
parents | 017c42b567ac |
children | 5eb62fb8a2d0 |
rev | line source |
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0
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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1 <tool id="pdaug_peptide_sequence_analysis" name="PDAUG Peptide Sequence Analysis" version="0.1.0"> |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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2 <description>Peptide sequence analysis</description> |
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3 |
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4 <requirements> |
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5 <requirement type="package" version="4.2.1">modlamp</requirement> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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6 <requirement type="package" version="1.0.5">pandas</requirement> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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7 <requirement type="package" version="4.10.0">plotly</requirement> |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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8 </requirements> |
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9 <stdio> |
e59674e3a391
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10 <exit_code range="1" level="fatal" /> |
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11 </stdio> |
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12 <command detect_errors="exit_code"><![CDATA[ |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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13 |
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14 |
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15 python '$__tool_directory__/PDAUG_Peptide_Sequence_Analysis.py' '$SelAnalysis.Analysis' |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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16 |
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17 #if $SelAnalysis.Analysis == 'CalcAAFreq' |
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18 --InFile '$SelAnalysis.input1' |
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19 --PlotFile '$output2' |
e59674e3a391
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20 --OutFile '$output1' |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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21 #end if |
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22 |
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23 #if $SelAnalysis.Analysis == 'H' |
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24 --InFile '$SelAnalysis.input1' |
017c42b567ac
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25 --Scale '$SelAnalysis.scale' |
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26 --OutFile '$output1' |
e59674e3a391
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27 #end if |
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28 |
e59674e3a391
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29 #if $SelAnalysis.Analysis == 'uH' |
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30 --InFile '$SelAnalysis.input1' |
017c42b567ac
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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31 --Scale '$SelAnalysis.Scale' |
017c42b567ac
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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32 --Window '$SelAnalysis.Window' |
017c42b567ac
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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33 --Angle '$SelAnalysis.Angle' |
017c42b567ac
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
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34 --Modality '$SelAnalysis.Modality' |
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35 --OutFile '$output1' |
e59674e3a391
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36 #end if |
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37 |
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38 #if $SelAnalysis.Analysis == 'charge' |
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39 --InFile '$SelAnalysis.input1' |
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40 --ph '$SelAnalysis.ph' |
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41 --Amide '$SelAnalysis.amide' |
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42 --OutFile '$output1' |
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43 |
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44 #end if |
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45 |
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46 #if $SelAnalysis.Analysis == 'Len' |
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47 --InFile '$SelAnalysis.input1' |
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48 --OutFile '$output1' |
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49 #end if |
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50 |
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51 #if $SelAnalysis.Analysis == 'PlotSummary' |
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52 --InFile1 '$SelAnalysis.input1' |
017c42b567ac
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53 --InFile2 '$SelAnalysis.input2' |
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54 --First_lib_name '$SelAnalysis.Pep1name' |
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55 --Second_lib_name '$SelAnalysis.Pep2name' |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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56 --htmlOutDir '$output2.extra_files_path' |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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57 --htmlFname '$output2' |
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58 #end if |
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59 |
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60 |
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61 ]]></command> |
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62 |
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63 |
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64 <inputs> |
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65 |
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66 <conditional name='SelAnalysis' > |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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67 |
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68 <param name="Analysis" type="select" label="Analysis options" argument=""> |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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69 <option value="CalcAAFreq">Calculate the amino acid frequency</option> |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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70 <option value="H">Calculate the global hydrophobicity</option> |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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71 <option value="uH">Calculating hydrophobic moments</option> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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72 <option value="charge">Calculate the total molecular charge</option> |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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73 <option value="Len">Calculate the sequence length</option> |
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74 <option value="PlotSummary">Plot Summary</option> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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75 </param> |
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76 |
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77 <when value="CalcAAFreq"> |
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78 <param name="input1" type="data" format="fasta" label="Input file" argument= "--InFile" help="Input fasta file with Peptides"/> |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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79 </when> |
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80 |
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81 <when value="H"> |
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82 <param name="input1" type="data" format="fasta" argument= "--InFile" label="Input file" help="Input fasta file with Peptides"/> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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83 <param name="scale" type="text" value="eisenberg" label="Hydrophobicity scale" help="Hydrophobicity scale"/> |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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84 </when> |
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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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85 |
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86 <when value="uH"> |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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87 <param name="input1" type="data" format="fasta" argument= "--InFile" label="Input file" help="Input fasta file with Peptides"/> |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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88 <param name="Scale" type="text" value="eisenberg" label="hydrophobicity scale" argument="--Scale" help="Hydrophobicity scale"/> |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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89 <param name="Window" type="integer" label="Window" value="1000" argument="--Window" help="Amino acid window in which to calculate the moment" /> |
e59674e3a391
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 6f53ad797ec1af02b41510063a86bec7d121abf3"
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90 <param name="Angle" type="integer" label="Angle" value="100" argument="--Angle" help="Angle in which to calculate the moment. 100 for alpha helices, 180 for beta sheets."/> |
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91 <param name="Modality" type="select" label="hydrophobicity scale" argument="--modality" help="Calculate respectively maximum or mean hydrophobic moment."> |
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92 <option value="max" >Max</option> |
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93 <option value="mean">Mean</option> |
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94 </param> |
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95 |
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96 </when> |
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97 |
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98 <when value="charge"> |
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99 <param name="input1" type="data" format="fasta" label="Input " argument= "--InFile" help="Input fasta file with Peptides"/> |
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100 <param name="ph" type="float" label="ph" value="7.0" help="--ph" /> |
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101 <param name="amide" type="boolean" label="amide" value="true" help="--Amide" /> |
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102 </when> |
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103 |
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104 <when value="Len"> |
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105 <param name="input1" type="data" format="fasta" argument= "--InFile" label="Input file" help="Input fasta file with Peptides"/> |
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106 </when> |
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107 |
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108 <when value="PlotSummary"> |
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109 <param name="input1" type="data" format="fasta" argument= "--InFile1" label="First input file" help="Input fasta file with Peptides"/> |
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110 <param name="input2" type="data" format="fasta" argument= "--InFile2" label="Second input file" help="Input fasta file with Peptides"/> |
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111 <param name="Pep1name" type="text" value="First data set" label="Name of the first dataset" help="Input fasta file with Peptides"/> |
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112 <param name="Pep2name" type="text" value="Second data set" label="Name of the second dataset" help="Input fasta file with Peptides"/> |
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113 </when> |
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114 </conditional> |
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115 </inputs> |
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116 |
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117 |
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118 <outputs> |
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119 <data name='output1' format='tabular' label="${tool.name} on $on_string - ${SelAnalysis.Analysis} (tabular)" > |
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120 |
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121 <filter>SelAnalysis['Analysis'] != "PlotSummary"</filter> |
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122 </data> |
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123 |
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124 |
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125 <data name='output2' format='html' label="${tool.name} on $on_string - ${SelAnalysis.Analysis} (webpage)" > |
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126 <filter>SelAnalysis['Analysis'] != "H"</filter> |
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127 <filter>SelAnalysis['Analysis'] != "uH"</filter> |
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128 <filter>SelAnalysis['Analysis'] != "charge"</filter> |
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129 <filter>SelAnalysis['Analysis'] != "Len"</filter> |
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130 <filter>SelAnalysis['Analysis'] != "CalcAAFreq"</filter> |
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131 </data> |
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132 |
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133 </outputs> |
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134 |
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135 <tests> |
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136 |
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137 |
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138 <test> |
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139 <param name="Analysis" value="CalcAAFreq" /> |
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140 <param name="input1" value="test1.fasta"/> |
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141 <output name="output1" file="test1/out.tsv"/> |
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142 </test> |
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143 |
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144 <test> |
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145 <param name="Analysis" value="H" /> |
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146 <param name="input1" value="test1.fasta"/> |
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147 <param name="scale" value="eisenberg"/> |
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148 <output name="output1" file="test2/out2.tsv"/> |
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149 </test> |
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150 |
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151 <test> |
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152 <param name="Analysis" value="uH" /> |
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153 <param name="input1" value="test1.fasta"/> |
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154 <param name="scale" value="eisenberg"/> |
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155 <param name="Window" value="1000"/> |
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156 <output name="output1" file="test3/out3.tsv"/> |
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157 </test> |
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158 |
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159 |
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160 <test> |
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161 <param name="Analysis" value="Len" /> |
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162 <param name="input1" value="test1.fasta"/> |
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163 <output name="output1" file="test5/out5.tsv"/> |
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164 </test> |
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165 |
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166 |
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167 <test> |
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168 <param name="Analysis" value="charge" /> |
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169 <param name="input1" value="test1.fasta"/> |
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170 <param name="ph" value="7.0" /> |
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171 <param name="amide" value="false" /> |
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172 <output name="output1" file="test6/out.tsv"/> |
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173 </test> |
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174 |
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175 <test> |
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176 <param name="Analysis" value="PlotSummary" /> |
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177 <param name="input1" value="non_ACPs.fasta"/> |
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178 <param name="input2" value="ACPs.fasta"/> |
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179 <param name="Pep1name" value="Non_ACP"/> |
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180 <param name="Pep2name" value="ACP" /> |
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181 <output name="output2" file="test4/report_dir/report.html.re" ftype="html" compare="re_match_multiline" /> |
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182 </test> |
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183 |
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184 </tests> |
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185 <help><![CDATA[ |
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186 .. class:: infomark |
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187 |
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188 **What it does** |
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189 |
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190 This module can be used for the diverse analysis of given peptide libraries and equiped with 6 different options. |
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191 |
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192 * **Calculate the amino acid frequency** Method to get the frequency of every amino acid in the library. If the library consists of sub-libraries, the frequencies of these are calculated independently. |
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193 * **Calculate the global hydrophobicity** Method for calculating global hydrophobicity (Eisenberg scale) of all sequences in the library. |
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194 * **Calculating hydrophobic moments** Method for calculating hydrophobic moments (Eisenberg scale) for all sequences in the library. |
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195 * **Calculate the total molecular charge** Method to calculate the total molecular charge at a given pH for all sequences in the library. |
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196 * **Calculate the sequence length** Method to get the sequence length of all sequences in the library. |
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197 * **Plot Summary** Method to generate a visual summary of different characteristics of the given library. The class methods are used with their standard options. |
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198 |
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199 |
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200 ----- |
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201 |
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202 **Inputs** |
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203 **1** Calculate the amino acid frequency |
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204 * **--InFile** Input fasta file with peptide sequences. |
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205 |
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206 **2** Calculate the global hydrophobicity |
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207 * **--InFile** Input fasta file with peptide sequences. |
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208 * **--Scale** Hydrophobicity scale to use. For available scales, see modlamp.descriptors.PeptideDescriptor. |
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209 |
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210 **3** Calculating hydrophobic moments |
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211 * **--InFile** Input fasta file with peptide sequences. |
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212 * **--Scale** Hydrophobicity scale to use. For available scales, see modlamp.descriptors.PeptideDescriptor. |
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213 * **--Window** amino acid window in which to calculate the moment. If the sequence is shorter than the window, the length of the sequence is taken. So if the default window of 1000 is chosen, for all sequences shorter than 1000, the global hydrophobic moment will be calculated. Otherwise, the maximal hydrophiobic moment for the chosen window size found in the sequence will be returned. |
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214 * **--Angle** angle in which to calculate the moment. 100 for alpha helices, 180 for beta sheets |
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215 * **--Modality** calculate respectively maximum or mean hydrophobic moment. |
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216 |
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217 **4** Calculate the total molecular charge |
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218 * **----InFile** Input fasta file with peptide sequences. |
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219 * **--ph** Input fasta file with peptide sequences. |
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220 * **--Amide** Whether the sequences have an amidated C-terminus (-> charge += 1). |
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221 |
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222 **5** Calculate the sequence length |
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223 * **--Infile** Input fasta file with peptides. |
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224 |
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225 **6** Plot Summary |
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226 * **--InFile1** First fasta file with peptide sequences. |
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227 * **--InFile2** Second Fasta file with peptides sequences. |
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228 |
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229 ----- |
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230 |
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231 **Outputs** |
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232 * **Calculate the amino acid frequency** Returns tabular file with html report file. |
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233 * **Calculate the global hydrophobicity** Returns tabular file. |
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234 * **Calculating hydrophobic moments** Returns tabular file. |
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235 * **Calculate the total molecular charge** Returns tabular file. |
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236 * **Calculate the sequence length** Returns tabular file. |
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237 * **Plot Summary** Return html report file. |
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238 |
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239 ]]></help> |
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240 <citations> |
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241 <citation type="bibtex"> |
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242 @misc{PDAUGGITHUB, |
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243 author = {Joshi, Jayadev and Blankenberg, Daniel}, |
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244 year = {2020}, |
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245 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, |
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246 publisher = {GitHub}, |
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247 journal = {GitHub repository}, |
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248 url = |
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249 {https://github.com/jaidevjoshi83/pdaug.git}, |
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250 } |
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251 </citation> |
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252 |
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253 <citation type="bibtex"> |
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254 @article{müller_gabernet_hiss_schneider_2017, |
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255 title={modlAMP: Python for antimicrobial peptides}, |
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256 volume={33}, |
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257 DOI={10.1093/bioinformatics/btx285}, |
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258 number={17}, |
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259 journal={Bioinformatics}, |
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260 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert}, |
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261 year={2017}, |
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262 pages={2753–2755} |
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263 } |
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264 </citation> |
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265 </citations> |
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266 </tool> |
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267 |
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268 |
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269 |