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annotate metafiles2pin.xml @ 0:3a49065a05d6 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
author galaxyp
date Wed, 07 Dec 2016 16:43:51 -0500
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
galaxyp
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1 <tool id="metafiles2pin" name="Merge search data" version="1.0">
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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2 <description>before creating percolator input</description>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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3 <stdio>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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4 <exit_code range="1:" />
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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5 </stdio>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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6 <command>python $__tool_directory__/metafiles2pin.py
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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7 --batchsize $percopoolsize
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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8 #if len($percopoolids) > 0
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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9 --percolator-pool-ids
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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10 #for $ppool in $percopoolids
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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11 "${ppool.ppool_identifier}"
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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12 #end for
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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13 #end if
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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14 --spectrafiles
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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15 #for $specfile in $searchresult.keys()
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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16 "$specfile"
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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17 #end for
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18 --searchfiles
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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19 #for $specfile in $searchresult.keys()
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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20 "$searchresult[$specfile]"
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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21 #end for
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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22 </command>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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23 <inputs>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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24 <param name="percopoolsize" type="integer" value="8" label="Amount of fractions to batch per Percolator process" />
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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25 <repeat name="percopoolids" title="Percolator pools" help="For cases where file amounts cause search results to not automatically line up into correct percolator batches">
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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26 <param name="ppool_identifier" type="text" label="Filename part identifying percolator pool"
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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27 help="Specify part of the input spectra filenames that are unique for each percolator pool, e.g set_A."/>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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28 </repeat>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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29 <param name="searchresult" type="data_collection" format="mzid" label="MSGF+, SQT or XTandem search results" />
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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30 </inputs>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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31 <outputs>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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32 <collection name="metafile_collection" type="list" label="Percolator metafiles list">
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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33 <discover_datasets pattern="__designation_and_ext__" directory="metafiles" />
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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34 </collection>
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35 </outputs>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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36 <tests>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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37 <test>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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38 <param name="percopoolsize" value="2"/>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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39 <param name="searchresult">
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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40 <collection type="list">
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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41 <element name="fraction_one_spectra" value="empty_file1.mzid"/>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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42 <element name="fraction_two_spectra" value="empty_file2.mzid"/>
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43 <element name="fraction_three_spectra" value="empty_file3.mzid"/>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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44 <element name="fraction_four_spectra" value="empty_file4.mzid"/>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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45 </collection>
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46 </param>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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47 <output_collection name="metafile_collection" type="list">
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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48 <element name="percolatorpool0">
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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49 <assert_contents>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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50 <has_text_matching expression="dataset_1.dat" />
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51 <has_text_matching expression="dataset_2.dat" />
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52 </assert_contents>
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53 </element>
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54 <element name="percolatorpool1">
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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55 <assert_contents>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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56 <has_text_matching expression="dataset_3.dat" />
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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57 <has_text_matching expression="dataset_4.dat" />
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58 </assert_contents>
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59 </element>
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60 </output_collection>
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61 </test>
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62 <test>
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63 <param name="percopoolsize" value="2"/>
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64 <repeat name="percopoolids">
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65 <param name="ppool_identifier" value="set1"/>
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66 </repeat>
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67 <repeat name="percopoolids">
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68 <param name="ppool_identifier" value="set2"/>
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69 </repeat>
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70 <param name="searchresult">
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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71 <collection type="list">
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72 <element name="fr_one_set1_spectra" value="empty_file1.mzid"/>
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73 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/>
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74 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/>
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75 <element name="fr_one_set2_spectra" value="empty_file4.mzid"/>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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76 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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77 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
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78 </collection>
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79 </param>
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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80 <output_collection name="metafile_collection" type="list">
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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81 <element name="percolatorpool0">
3a49065a05d6 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b4871f9659a924a68430aed3a93f4f9bad733fd6
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82 <assert_contents>
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83 <has_text_matching expression="dataset_7.dat" />
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84 <has_text_matching expression="dataset_8.dat" />
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85 </assert_contents>
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86 </element>
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87 <element name="percolatorpool1">
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88 <assert_contents>
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89 <has_text_matching expression="dataset_9.dat" />
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90 </assert_contents>
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91 </element>
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92 <element name="percolatorpool2">
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93 <assert_contents>
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94 <has_text_matching expression="dataset_10.dat" />
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95 <has_text_matching expression="dataset_11.dat" />
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96 </assert_contents>
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97 </element>
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98 <element name="percolatorpool3">
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99 <assert_contents>
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100 <has_text_matching expression="dataset_12.dat" />
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101 </assert_contents>
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102 </element>
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103 </output_collection>
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104 </test>
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105 </tests>
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106 <help>
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107 Creates meta files containing the filenames of the search data in batches of
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108 a specific size. These are used as inputs to sqt2pin, msgfplus2pin or tandem2pin.
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109 Use this feature when you want to batch a specific amount of input search results
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110 to run in percolator, as opposed to one at a time. This tool generates a collection
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111 containing multiple batches of the search results. You can specify batch size as well
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112 as a pattern in the spectra files which makes sure the batching isn't continued through
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113 very different MS sets. Instead, for each filename-pattern it generates batches of the
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114 specified size.
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115 </help>
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116 </tool>