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annotate msgf2pin.xml @ 1:86770eea5b09 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
author galaxyp
date Sat, 04 Mar 2017 20:36:03 -0500
parents 3a49065a05d6
children
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86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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1 <tool id="msgfplus2pin" name="MS-GF+ output to Pin converter" version="3.0.1">
0
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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2 <description>to create Percolator input files</description>
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3 <requirements>
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4 <requirement type="package" version="3.0">percolator</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:"/>
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8 </stdio>
1
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9 <command><![CDATA[
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10 mkdir target && mkdir decoy &&
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11
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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12 #if $mzids.inputtype == "multi"
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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13 #for $key in $mzids.target.keys()
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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14 ln -s '$mzids.target[$key]' 'target/$key' &&
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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15 echo 'target/$key' >> targetmeta &&
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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16 #end for
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17 #for $key in $mzids.decoy.keys()
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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18 ln -s '$mzids.decoy[$key]' 'decoy/$key' &&
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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19 echo 'decoy/$key' >> decoymeta &&
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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20 #end for
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21 msgf2pin -o $pinout -e $enzyme
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22 #if $matches
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23 -m $matches
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24 #end if
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25 $aafreq $ptm $pngase $isotope targetmeta decoymeta
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26
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27 #else
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28 ln -s '$mzids.target' 'target/$target.display_name' &&
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29 ln -s '$mzids.decoy' 'decoy/$decoy.display_name' &&
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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30 msgf2pin -o $pinout -e $enzyme
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31 #if $matches
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32 -m $matches
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33 #end if
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34 $aafreq $ptm $pngase $isotope
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35 'target/$mzids.target.display_name' 'decoy/$mzids.decoy.display_name'
0
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36 #end if
1
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37 ]]></command>
0
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38 <inputs>
1
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39 <conditional name="mzids">
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40 <param name="inputtype" type="select" display="radio">
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41 <option value="single">Single mzIdentML</option>
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42 <option value="multi">Multiple mzIdentMLs</option>
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43 </param>
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44 <when value="single">
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45 <param name="target" type="data" format="mzid" label="Target MSGF+ results" />
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46 <param name="decoy" type="data" format="mzid" label="Decoy MSGF+ results" />
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47 </when>
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48 <when value="multi">
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49 <param name="target" type="data_collection" collection_type="list" format="mzid" label="Target MSGF+ results" />
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50 <param name="decoy" type="data_collection" collection_type="list" format="mzid" label="Decoy MSGF+ results" />
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51 </when>
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52 </conditional>
0
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53 <param name="enzyme" type="select" label="Enzyme used">
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54 <option value="trypsin">trypsin</option>
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55 <option value="no_enzyme">no enzyme</option>
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56 <option value="elastase">elastase</option>
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57 <option value="pepsin">pepsin</option>
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58 <option value="proteinasek">proteinase K</option>
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59 <option value="thermolysin">thermolysin</option>
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60 <option value="chymotrypsin">chymotrypsin</option>
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61 <option value="lys-n">lys-N</option>
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62 <option value="lys-c">lys-C</option>
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63 <option value="arg-c">arg-C</option>
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64 <option value="asp-n">asp-N</option>
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65 <option value="glu-c">glu-C</option>
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66 </param>
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67 <param name="matches" type="integer" optional="true" label="Max number of PSMs for a spectrum" />
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68 <param name="aafreq" type="boolean" label="Calculate amino acid frequency features" truevalue="-a" falsevalue="" />
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69 <param name="ptm" type="boolean" label="Calculate feature for number of PTMs" truevalue="-b" falsevalue="" />
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70 <param name="pngase" type="boolean" label="Calculate feature based on N-linked glycosylation resulting from PNGaseF" truevalue="-N" falsevalue="" />
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71 <param name="isotope" type="boolean" label="Calculate mass difference to closest isotope instead of avg. mass" truevalue="-M" falsevalue="" />
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72 </inputs>
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73 <outputs>
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74 <data format="percin" name="pinout"/>
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75 </outputs>
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76 <tests>
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77 <test>
1
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78 <param name="mzids|inputtype" value="single" />
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79 <param name="mzids|target" value="target.mzid" />
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80 <param name="mzids|decoy" value="decoy.mzid" />
0
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81 <param name="ptm" value="true"/>
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82 <param name="matches" value="1"/>
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83 <output name="pinout" value="percolatorInresult.txt" compare="sim_size" delta="20" />
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84 </test>
1
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85 <test>
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86 <param name="mzids|inputtype" value="multi" />
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87 <param name="mzids|target">
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88 <collection type="list">
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89 <element name="target1" value="target.mzid" />
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90 <element name="target2" value="target.mzid" />
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91 </collection>
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92 </param>
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93 <param name="mzids|decoy">
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94 <collection type="list">
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95 <element name="decoy1" value="decoy.mzid" />
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96 <element name="decoy2" value="decoy.mzid" />
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97 </collection>
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98 </param>
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99 <param name="ptm" value="true"/>
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100 <param name="matches" value="1"/>
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101 <output name="pinout" value="percolatorInresult_multifractions.txt" compare="sim_size" delta="20" />
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102 </test>
0
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103 </tests>
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104 <help>
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105 The percolator converter msgf2pin converts mzIdentML to input for percolator.
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106 Target and decoy inputs are MzIdentML-files of MS-GF+ from
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107 separate target and decoy searches. Internal MS-GF+ target/decoy
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108 analysis should be turned off, and the addFeatures options turned on.
1
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109 Multiple MzIdentML-files can be merged by passing lists of these.
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110 For successful results, the different runs should be generated under
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111 similar conditions.
0
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112 </help>
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113 <citations>
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114 <citation type="doi">10.1021/pr400937n</citation>
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115 </citations>
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116 </tool>