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

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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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77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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1 <tool id="pi_db_split" name="Split peptide database" version="1.2">
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2 <description>into pI separated fractions</description>
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3 <requirements>
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4 <requirement type="package">numpy</requirement>
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5 <requirement type="package" version="3.6">python</requirement>
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6 </requirements>
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9 mkdir pi_fr_out && cd pi_fr_out &&
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10 python '$__tool_directory__/pi_database_splitter.py' -i '$pipeptides' -p '$peptable'
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11 #for $strip in $strips
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12 #if not $strip.peptable_pattern or str($strip.peptable_pattern) in $peptable.element_identifier
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13 --intercept $strip.intercept --width $strip.fr_width --tolerance $strip.tolerance --amount $strip.fr_amount --prefix pisplit --picutoff $strip.picutoff
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14 #if $strip.reverse
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15 --reverse
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16 #end if
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17 #break
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18 #end if
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19 #end for
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21 #if $deltacol
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22 --deltacol $deltacol
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23 #else if $deltacolpattern
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24 --deltacolpattern '$deltacolpattern'
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25 #end if
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26 #if $fdrcol
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27 --fdrcol $fdrcol --fdrcutoff $fdrcutoff
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28 #else if $fdrcolpattern
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29 --fdrcolpattern '$fdrcolpattern' --fdrcutoff $fdrcutoff
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30 #end if
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31 #if $maxlen
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32 --maxlen $maxlen
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33 #end if
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34 --minlen $minlen
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35 ]]>
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36 </command>
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37
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38 <inputs>
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39 <param name="pipeptides" type="data" format="tabular" label="Target peptides with pI and accession" help="First col accession, second sequence, third pI" />
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40 <param name="peptable" type="data" format="tabular" label="Peptide table to determine pI shift from" help="Should have delta pI as a column" />
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41 <param name="fdrcolpattern" type="text" optional="true" label="FDR (q-value) column pattern in peptide table" />
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42 <param name="fdrcol" type="integer" value="" optional="true" label="FDR (q-value) column number in peptide table" help="Overrides column pattern if filled. First column is 1" />
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43 <param name="fdrcutoff" type="float" value="0.0" help="Not used when no FDR column specified" label="FDR value cutoff for inclusion in shift determination" />
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44 <param name="deltacolpattern" type="text" value="" label="Delta pI column pattern in peptide table" />
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45 <param name="deltacol" type="integer" optional="true" value="" label="Delta pI column number in peptide table" help="Overrides column pattern if filled. First column is 1"/>
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46 <param name="minlen" type="integer" value="8" label="Minimum length of peptide to include in split DB" />
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47 <param name="maxlen" type="integer" optional="true" value="" label="Max. length of peptide to include in split DB" />
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48 <repeat name="strips" title="pI separation strip data">
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49 <param name="peptable_pattern" type="text" label="Pattern to find correct peptide table for a strip, for when multiple peptide tables have different strips" help="Will match against peptide table's name. Leave blank for single peptide table or when using same strip in all tables" />
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50 <param name="intercept" type="float" value="" label="Intercept of pI strip" />
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51 <param name="fr_width" type="float" value="" label="Fraction width" />
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52 <param name="tolerance" type="float" value="" label="pI tolerance" />
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53 <param name="fr_amount" type="integer" value="" label="Fraction amount" />
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54 <param name="reverse" type="boolean" label="Strip is reversed (high-to-low pI)?" />
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55 <param name="picutoff" type="float" value="0.2" optional="true" label="delta-pI cutoff for inclusion in shift determination" />
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56 </repeat>
0
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57 </inputs>
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58
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59 <outputs>
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60 <collection name="target_pi_db" type="list" label="target pI separated db">
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61 <discover_datasets pattern="pisplit_(?P&lt;designation&gt;.+)\.fasta" ext="fasta" directory="pi_fr_out" />
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62 </collection>
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63 <collection name="decoy_pi_db" type="list" label="decoy pI separated db">
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64 <discover_datasets pattern="decoy_pisplit_(?P&lt;designation&gt;.+)\.fasta" ext="fasta" directory="pi_fr_out" />
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65 </collection>
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66 </outputs>
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67 <tests>
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68 <test>
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69 <param name="pipeptides" value="predicted_peptides_to_split.txt" />
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70 <param name="peptable" value="peptable_deltapi.txt" />
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71 <param name="fdrcol" value="3" />
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72 <param name="fdrcutoff" value="0.2" />
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73 <param name="deltacol" value="-1" />
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74 <param name="minlen" value="8" />
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75 <repeat name="strips">
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76 <param name="peptable_pattern" value="deltapi" />
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77 <param name="intercept" value="5.6" />
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78 <param name="fr_width" value="1.3" />
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79 <param name="tolerance" value="0.1" />
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80 <param name="fr_amount" value="3" />
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81 <param name="reverse" value="false" />
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82 <param name="picutoff" value="10" />
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83 </repeat>
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84 <output_collection name="target_pi_db" type="list">
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85 <element name="fr1" value="target_splitdb_fr1.fasta" />
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86 <element name="fr2" value="target_splitdb_fr2.fasta" />
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87 <element name="fr3" value="target_splitdb_fr3.fasta" />
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88 </output_collection>
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89 <output_collection name="decoy_pi_db" type="list">
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90 <element name="fr1" value="decoy_splitdb_fr1.fasta" />
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91 <element name="fr2" value="decoy_splitdb_fr2.fasta" />
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92 <element name="fr3" value="decoy_splitdb_fr3.fasta" />
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93 </output_collection>
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94 </test>
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95 <test>
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96 <param name="pipeptides" value="predicted_peptides_to_split.txt" />
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97 <param name="peptable" value="peptable_deltapi.txt" />
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98 <param name="fdrcolpattern" value="FDR" />
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99 <param name="fdrcutoff" value="0.2" />
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100 <param name="deltacolpattern" value="Delta" />
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101 <param name="minlen" value="8" />
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102 <repeat name="strips">
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103 <param name="intercept" value="5.6" />
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104 <param name="fr_width" value="1.3" />
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105 <param name="tolerance" value="0.1" />
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106 <param name="fr_amount" value="3" />
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107 <param name="reverse" value="false" />
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108 <param name="picutoff" value="10" />
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109 </repeat>
0
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110 <output_collection name="target_pi_db" type="list">
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111 <element name="fr1" value="target_splitdb_fr1.fasta" />
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112 <element name="fr2" value="target_splitdb_fr2.fasta" />
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113 <element name="fr3" value="target_splitdb_fr3.fasta" />
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114 </output_collection>
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115 <output_collection name="decoy_pi_db" type="list">
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116 <element name="fr1" value="decoy_splitdb_fr1.fasta" />
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117 <element name="fr2" value="decoy_splitdb_fr2.fasta" />
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118 <element name="fr3" value="decoy_splitdb_fr3.fasta" />
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119 </output_collection>
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120 </test>
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121 </tests>
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122
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123 <help>
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124 Creates a pI separated database collection from a pI-determined input
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125 file of peptide/protein mappings. Outputs one db for target, one
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126 for decoy.
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127 </help>
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128
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129 </tool>