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

"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 dce55ca21b98
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1 <tool id="batched_set_list_creator" name="Create nested list" version="3.3">
1
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2 <description>based on filenames and batch sizes</description>
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3 <stdio>
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4 <exit_code range="1:" />
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5 </stdio>
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6 <command>python $__tool_directory__/nested_collection.py
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7 #if $batchsize
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8 --batchsize $batchsize
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9 #end if
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10 #if len($poolids) > 0
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11 --pool-ids
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12 #for $pool in $poolids
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13 '${pool.pool_identifier}'
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14 #end for
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15 #end if
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16 --real-names
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17 #for $fname in $listtobatch.keys()
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18 '$fname'
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19 #end for
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20 --galaxy-files
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21 #for $fname in $listtobatch.keys()
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22 '$listtobatch[$fname]'
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23 #end for
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24 </command>
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25 <inputs>
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26 <param name="batchsize" type="integer" optional="true" value="" label="Maximal amount of fractions to batch." help="No value means no maximum" />
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27 <param name="filetype" type="select" label="Which datatype to nest?">
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28 <option value="mzid">mzIdentML</option>
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29 <option value="percout">Percolator out</option>
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30 <option value="tabular">Tabular</option>
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31 </param>
1
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32 <repeat name="poolids" title="Batch pools" help="Pools containing batches (optional, not using this will result in one pool)">
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33 <param name="pool_identifier" type="text" label="Filename part identifying batchpool"
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34 help="Specify part of the input filenames that are unique for each pool, e.g set_A. Do not use 3 consecutive underscores."/>
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35 </repeat>
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36 <param name="listtobatch" type="data_collection" collection_type="list" label="List of files to batch" />
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37 </inputs>
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38 <outputs>
3
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39 <collection name="batched_fractions_mzid" type="list:list" label="Pooled batched mzIdentML data">
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40 <filter>filetype == "mzid"</filter>
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41 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.-]+)\.data" ext="mzid" visible="false" />
3
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42 </collection>
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43 <collection name="batched_fractions_perco" type="list:list" label="Pooled batched percolator data">
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44 <filter>filetype == "percout"</filter>
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45 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.-]+)\.data" ext="percout" visible="false" />
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46 </collection>
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47 <collection name="batched_fractions_tab" type="list:list" label="Pooled batched tabular data">
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48 <filter>filetype == "tabular"</filter>
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49 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.-]+)\.data" ext="tabular" visible="false" />
1
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50 </collection>
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51 </outputs>
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52 <tests>
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53 <test>
4
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54 <param name="batchsize" value="6"/>
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55 <param name="filetype" value="mzid" />
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56 <param name="listtobatch">
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57 <collection type="list">
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58 <element name="fraction_one_spectra.mzML" value="empty_file1.mzid"/>
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59 <element name="fraction_two_spectra" value="empty_file2.mzid"/>
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60 <element name="fraction_three_spectra" value="empty_file3.mzid"/>
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61 <element name="fraction_four_spectra" value="empty_file4.mzid"/>
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62 <element name="fraction_five_spectra" value="empty_file5.mzid"/>
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63 <element name="fraction_six_spectra" value="empty_file6.mzid"/>
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64 <element name="fraction_seven_spectra" value="empty_file7.mzid"/>
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65 <element name="fraction_eight_spectra" value="empty_file8.mzid"/>
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66 <element name="fraction_nine_spectra" value="empty_file9.mzid"/>
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67 <element name="fraction_ten_spectra" value="empty_file10.mzid"/>
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68 <element name="fraction_eleven_spectra" value="empty_file11.mzid"/>
1
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69 </collection>
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70 </param>
3
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71 <output_collection name="batched_fractions_mzid" type="list:list">
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72 <element name="pool0_batch0">
4
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73 <element name="inputfn00_fraction_one_spectra.mzML" ftype="mzid" file="empty_file1.mzid"/>
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74 <element name="inputfn01_fraction_two_spectra" ftype="mzid" file="empty_file2.mzid"/>
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75 <element name="inputfn02_fraction_three_spectra" ftype="mzid" file="empty_file3.mzid"/>
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76 <element name="inputfn03_fraction_four_spectra" ftype="mzid" file="empty_file4.mzid"/>
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77 <element name="inputfn04_fraction_five_spectra" ftype="mzid" file="empty_file5.mzid"/>
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78 <element name="inputfn05_fraction_six_spectra" ftype="mzid" file="empty_file6.mzid"/>
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79 </element>
2
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80 <element name="pool0_batch1">
4
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81 <element name="inputfn06_fraction_seven_spectra" ftype="mzid" file="empty_file7.mzid"/>
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82 <element name="inputfn07_fraction_eight_spectra" ftype="mzid" file="empty_file8.mzid"/>
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83 <element name="inputfn08_fraction_nine_spectra" ftype="mzid" file="empty_file9.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
diff changeset
84 <element name="inputfn09_fraction_ten_spectra" ftype="mzid" file="empty_file10.mzid"/>
6
07107a686ce9 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit de8cdf895c3c6113f301a119788701b2465a1b1b"
galaxyp
parents: 5
diff changeset
85 <element name="inputfn10_fraction_eleven_spectra" ftype="mzid" file="empty_file11.mzid"/>
1
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff changeset
86 </element>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff changeset
87 </output_collection>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
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88 </test>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff changeset
89 <test>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff changeset
90 <repeat name="poolids">
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
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91 <param name="pool_identifier" value="set1"/>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
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92 </repeat>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff changeset
93 <repeat name="poolids">
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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94 <param name="pool_identifier" value="set2"/>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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95 </repeat>
3
abed51712ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
parents: 2
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96 <param name="filetype" value="tabular" />
1
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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97 <param name="listtobatch">
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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98 <collection type="list">
5
dce55ca21b98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4fd46e83045d78a4703c0ae7d0cfc396bdbc8e78
galaxyp
parents: 4
diff changeset
99 <element name="fr_one_set1-spectra" value="empty_file1.mzid"/>
1
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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100 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
diff changeset
101 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/>
4
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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diff changeset
102 <element name="fr_four_set1_spectra" value="empty_file4.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
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103 <element name="fr_five_set1_spectra" value="empty_file5.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
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104 <element name="fr_six_set1_spectra" value="empty_file6.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
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105 <element name="fr_seven_set1_spectra" value="empty_file7.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
diff changeset
106 <element name="fr_eight_set1_spectra" value="empty_file8.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
diff changeset
107 <element name="fr_nine_set1_spectra" value="empty_file9.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
diff changeset
108 <element name="fr_ten_set1_spectra" value="empty_file10.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
diff changeset
109 <element name="fr_eleven_set1_spectra" value="empty_file11.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
diff changeset
110 <element name="fr_one_set2_spectra" value="empty_file12.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
diff changeset
111 <element name="fr_two_set2_spectra" value="empty_file13.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
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112 <element name="fr_three_set2_spectra" value="empty_file14.mzid"/>
1
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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113 </collection>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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114 </param>
3
abed51712ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
galaxyp
parents: 2
diff changeset
115 <output_collection name="batched_fractions_tab" type="list:list">
2
7a0951d0e13e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038
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parents: 1
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116 <element name="set1_batch0">
5
dce55ca21b98 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4fd46e83045d78a4703c0ae7d0cfc396bdbc8e78
galaxyp
parents: 4
diff changeset
117 <element name="inputfn00_fr_one_set1-spectra" ftype="tabular" file="empty_file1.mzid"/>
4
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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118 <element name="inputfn01_fr_two_set1_spectra" ftype="tabular" file="empty_file2.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
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119 <element name="inputfn02_fr_three_set1_spectra" ftype="tabular" file="empty_file3.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
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120 <element name="inputfn03_fr_four_set1_spectra" ftype="tabular" file="empty_file4.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
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121 <element name="inputfn04_fr_five_set1_spectra" ftype="tabular" file="empty_file5.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
diff changeset
122 <element name="inputfn05_fr_six_set1_spectra" ftype="tabular" file="empty_file6.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
diff changeset
123 <element name="inputfn06_fr_seven_set1_spectra" ftype="tabular" file="empty_file7.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
diff changeset
124 <element name="inputfn07_fr_eight_set1_spectra" ftype="tabular" file="empty_file8.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
diff changeset
125 <element name="inputfn08_fr_nine_set1_spectra" ftype="tabular" file="empty_file9.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
diff changeset
126 <element name="inputfn09_fr_ten_set1_spectra" ftype="tabular" file="empty_file10.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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diff changeset
127 <element name="inputfn10_fr_eleven_set1_spectra" ftype="tabular" file="empty_file11.mzid"/>
1
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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128 </element>
2
7a0951d0e13e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038
galaxyp
parents: 1
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129 <element name="set2_batch1">
4
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
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130 <element name="inputfn0_fr_one_set2_spectra" ftype="tabular" file="empty_file12.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
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131 <element name="inputfn1_fr_two_set2_spectra" ftype="tabular" file="empty_file13.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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132 <element name="inputfn2_fr_three_set2_spectra" ftype="tabular" file="empty_file14.mzid"/>
1
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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133 </element>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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134 </output_collection>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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135 </test>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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136 <test>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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137 <param name="batchsize" value="2"/>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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138 <repeat name="poolids">
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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139 <param name="pool_identifier" value="set1"/>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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140 </repeat>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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141 <repeat name="poolids">
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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142 <param name="pool_identifier" value="set2"/>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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143 </repeat>
3
abed51712ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
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144 <param name="filetype" value="percout" />
1
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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145 <param name="listtobatch">
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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146 <collection type="list">
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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147 <element name="fr_one_set1_spectra" value="empty_file1.mzid"/>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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148 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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149 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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150 <element name="fr_one_set2_spectra" value="empty_file4.mzid"/>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
parents:
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151 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
galaxyp
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152 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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153 </collection>
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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154 </param>
3
abed51712ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
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155 <output_collection name="batched_fractions_perco" type="list:list">
2
7a0951d0e13e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038
galaxyp
parents: 1
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156 <element name="set1_batch0">
4
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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parents: 3
diff changeset
157 <element name="inputfn0_fr_one_set1_spectra" ftype="percout" file="empty_file1.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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158 <element name="inputfn1_fr_two_set1_spectra" ftype="percout" file="empty_file2.mzid"/>
1
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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159 </element>
2
7a0951d0e13e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038
galaxyp
parents: 1
diff changeset
160 <element name="set1_batch1">
4
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
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161 <element name="inputfn2_fr_three_set1_spectra" ftype="percout" file="empty_file3.mzid"/>
1
86770eea5b09 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
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162 </element>
2
7a0951d0e13e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038
galaxyp
parents: 1
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163 <element name="set2_batch2">
4
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
parents: 3
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164 <element name="inputfn0_fr_one_set2_spectra" ftype="percout" file="empty_file4.mzid"/>
154147805a33 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
galaxyp
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165 <element name="inputfn1_fr_two_set2_spectra" ftype="percout" file="empty_file5.mzid"/>
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166 </element>
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167 <element name="set2_batch3">
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168 <element name="inputfn2_fr_three_set2_spectra" ftype="percout" file="empty_file6.mzid"/>
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169 </element>
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170 </output_collection>
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171 </test>
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172 </tests>
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173 <help>
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174 Creates nested collection containing from a list containing datasets in batches of
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175 a specific size. Useful when e.g. creating inputs to sqt2pin, msgfplus2pin or tandem2pin.
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176 Use this feature when you want to batch a specific amount of datasets, or datasets with
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177 a common file name pattern, or both.
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178 The tool generates a collection containing batches which contain multiple batches
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179 of input files. The pools are specified as a pattern in the input
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180 files which makes sure the batching isn't continued through very different input sets
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181 if that is a problem. Instead, for each filename-pattern it generates batches of the
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182 specified size.
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183 </help>
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184 </tool>