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annotate percolator_converters.xml @ 6:07107a686ce9 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit de8cdf895c3c6113f301a119788701b2465a1b1b"
author galaxyp
date Thu, 13 Aug 2020 03:53:33 -0400
parents 7a0951d0e13e
children
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6
07107a686ce9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit de8cdf895c3c6113f301a119788701b2465a1b1b"
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1 <tool id="percolator_input_converters" name="Search engine output to Pin converter" version="@TOOL_VERSION@+galaxy0">
2
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2 <description>to create Percolator input files</description>
6
07107a686ce9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit de8cdf895c3c6113f301a119788701b2465a1b1b"
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3 <macros>
07107a686ce9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit de8cdf895c3c6113f301a119788701b2465a1b1b"
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4 <import>percolator_macros.xml</import>
07107a686ce9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit de8cdf895c3c6113f301a119788701b2465a1b1b"
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5 </macros>
07107a686ce9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit de8cdf895c3c6113f301a119788701b2465a1b1b"
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6 <expand macro="requirements" />
2
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7 <stdio>
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8 <exit_code range="1:"/>
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9 </stdio>
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10 <command><![CDATA[
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11 mkdir target && mkdir decoy &&
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12
7a0951d0e13e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038
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13 #if $mzids.inputtype == "multi"
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14 #for $key in $mzids.target.keys()
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15 ln -s '$mzids.target[$key]' 'target/$key' &&
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16 echo 'target/$key' >> targetmeta &&
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17 #end for
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18 #for $key in $mzids.decoy.keys()
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19 ln -s '$mzids.decoy[$key]' 'decoy/$key' &&
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20 echo 'decoy/$key' >> decoymeta &&
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21 #end for
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22 $searchengine -o $pinout -e $enzyme
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23 #if $matches
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24 -m $matches
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25 #end if
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26 $aafreq $ptm $pngase $isotope targetmeta decoymeta
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27
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28 #else
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29 ln -s '$mzids.target' 'target/$target.display_name' &&
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30 ln -s '$mzids.decoy' 'decoy/$decoy.display_name' &&
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31 $searchengine -o $pinout -e $enzyme
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32 #if $matches
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33 -m $matches
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34 #end if
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35 $aafreq $ptm $pngase $isotope
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36 'target/$mzids.target.display_name' 'decoy/$mzids.decoy.display_name'
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37 #end if
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38 ]]></command>
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39 <inputs>
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40 <param name="searchengine" type="select" label="Search engine used">
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41 <option value="msgf2pin">MSGF+ (mzIdentML)</option>
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42 <option value="tandem2pin">X!Tandem (tandem)</option>
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43 <option value="sqt2pin">Crux (SQT output)</option>
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44 </param>
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45 <conditional name="mzids">
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46 <param name="inputtype" type="select" display="radio">
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47 <option value="single">Single mzIdentML</option>
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48 <option value="multi">Multiple mzIdentMLs</option>
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49 </param>
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50 <when value="single">
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51 <param name="target" type="data" format="mzid" label="Target MSGF+ results" />
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52 <param name="decoy" type="data" format="mzid" label="Decoy MSGF+ results" />
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53 </when>
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54 <when value="multi">
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55 <param name="target" type="data_collection" collection_type="list" format="mzid" label="Target MSGF+ results" />
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56 <param name="decoy" type="data_collection" collection_type="list" format="mzid" label="Decoy MSGF+ results" />
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57 </when>
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58 </conditional>
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59 <param name="enzyme" type="select" label="Enzyme used">
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60 <option value="trypsin">trypsin</option>
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61 <option value="no_enzyme">no enzyme</option>
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62 <option value="elastase">elastase</option>
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63 <option value="pepsin">pepsin</option>
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64 <option value="proteinasek">proteinase K</option>
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65 <option value="thermolysin">thermolysin</option>
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66 <option value="chymotrypsin">chymotrypsin</option>
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67 <option value="lys-n">lys-N</option>
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68 <option value="lys-c">lys-C</option>
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69 <option value="arg-c">arg-C</option>
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70 <option value="asp-n">asp-N</option>
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71 <option value="glu-c">glu-C</option>
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72 </param>
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73 <param name="matches" type="integer" optional="true" label="Max number of PSMs for a spectrum" />
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74 <param name="aafreq" type="boolean" label="Calculate amino acid frequency features" truevalue="-a" falsevalue="" />
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75 <param name="ptm" type="boolean" label="Calculate feature for number of PTMs" truevalue="-b" falsevalue="" />
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76 <param name="pngase" type="boolean" label="Calculate feature based on N-linked glycosylation resulting from PNGaseF" truevalue="-N" falsevalue="" />
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77 <param name="isotope" type="boolean" label="Calculate mass difference to closest isotope instead of avg. mass" truevalue="-M" falsevalue="" />
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78 </inputs>
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79 <outputs>
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80 <data format="percin" name="pinout"/>
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81 </outputs>
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82 <tests>
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83 <test>
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84 <param name="mzids|inputtype" value="single" />
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85 <param name="mzids|target" value="target.mzid" />
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86 <param name="mzids|decoy" value="decoy.mzid" />
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87 <param name="ptm" value="true"/>
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88 <param name="matches" value="1"/>
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89 <output name="pinout" value="percolatorInresult.txt" compare="sim_size" delta="20" />
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90 </test>
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91 <test>
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92 <param name="mzids|inputtype" value="multi" />
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93 <param name="mzids|target">
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94 <collection type="list">
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95 <element name="target1" value="target.mzid" />
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96 <element name="target2" value="target.mzid" />
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97 </collection>
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98 </param>
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99 <param name="mzids|decoy">
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100 <collection type="list">
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101 <element name="decoy1" value="decoy.mzid" />
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102 <element name="decoy2" value="decoy.mzid" />
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103 </collection>
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104 </param>
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105 <param name="ptm" value="true"/>
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106 <param name="matches" value="1"/>
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107 <output name="pinout" value="percolatorInresult_multifractions.txt" compare="sim_size" delta="20" />
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108 </test>
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109 </tests>
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110 <help>
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111 The percolator converter msgf2pin converts mzIdentML to input for percolator.
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112 Target and decoy inputs are MzIdentML-files of MS-GF+ from
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113 separate target and decoy searches. Internal MS-GF+ target/decoy
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114 analysis should be turned off, and the addFeatures options turned on.
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115 Multiple MzIdentML-files can be merged by passing lists of these.
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116 For successful results, the different runs should be generated under
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117 similar conditions.
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118 </help>
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119 <citations>
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120 <citation type="doi">10.1021/pr400937n</citation>
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121 </citations>
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122 </tool>