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comparison nested_collection.xml @ 6:65b285f9f7ad draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit f7c987a36f3604b735bd0b288630045a05e0bc4d-dirty
author jorritb
date Fri, 19 May 2017 08:40:46 -0400
parents 44e32e51ff94
children
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5:44e32e51ff94 6:65b285f9f7ad
1 <tool id="batched_set_list_creator" name="Create nested list" version="3.2"> 1 <tool id="batched_set_list_creator" name="Create nested list" version="3.3">
2 <description>based on filenames and batch sizes</description> 2 <description>based on filenames and batch sizes</description>
3 <stdio> 3 <stdio>
4 <exit_code range="1:" /> 4 <exit_code range="1:" />
5 </stdio> 5 </stdio>
6 <command>python $__tool_directory__/nested_collection.py 6 <command>python $__tool_directory__/nested_collection.py
36 <param name="listtobatch" type="data_collection" collection_type="list" label="List of files to batch" /> 36 <param name="listtobatch" type="data_collection" collection_type="list" label="List of files to batch" />
37 </inputs> 37 </inputs>
38 <outputs> 38 <outputs>
39 <collection name="batched_fractions_mzid" type="list:list" label="Pooled batched mzIdentML data"> 39 <collection name="batched_fractions_mzid" type="list:list" label="Pooled batched mzIdentML data">
40 <filter>filetype == "mzid"</filter> 40 <filter>filetype == "mzid"</filter>
41 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.]+)\.data" ext="mzid" visible="false" /> 41 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.-]+)\.data" ext="mzid" visible="false" />
42 </collection> 42 </collection>
43 <collection name="batched_fractions_perco" type="list:list" label="Pooled batched percolator data"> 43 <collection name="batched_fractions_perco" type="list:list" label="Pooled batched percolator data">
44 <filter>filetype == "percout"</filter> 44 <filter>filetype == "percout"</filter>
45 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.]+)\.data" ext="percout" visible="false" /> 45 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.-]+)\.data" ext="percout" visible="false" />
46 </collection> 46 </collection>
47 <collection name="batched_fractions_tab" type="list:list" label="Pooled batched tabular data"> 47 <collection name="batched_fractions_tab" type="list:list" label="Pooled batched tabular data">
48 <filter>filetype == "tabular"</filter> 48 <filter>filetype == "tabular"</filter>
49 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.]+)\.data" ext="tabular" visible="false" /> 49 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[\w.-]+)\.data" ext="tabular" visible="false" />
50 </collection> 50 </collection>
51 </outputs> 51 </outputs>
52 <tests> 52 <tests>
53 <test> 53 <test>
54 <param name="batchsize" value="6"/> 54 <param name="batchsize" value="6"/>
55 <param name="filetype" value="mzid" /> 55 <param name="filetype" value="mzid" />
56 <param name="listtobatch"> 56 <param name="listtobatch">
57 <collection type="list"> 57 <collection type="list">
58 <element name="fraction_one_spectra" value="empty_file1.mzid"/> 58 <element name="fraction_one_spectra.mzML" value="empty_file1.mzid"/>
59 <element name="fraction_two_spectra" value="empty_file2.mzid"/> 59 <element name="fraction_two_spectra" value="empty_file2.mzid"/>
60 <element name="fraction_three_spectra" value="empty_file3.mzid"/> 60 <element name="fraction_three_spectra" value="empty_file3.mzid"/>
61 <element name="fraction_four_spectra" value="empty_file4.mzid"/> 61 <element name="fraction_four_spectra" value="empty_file4.mzid"/>
62 <element name="fraction_five_spectra" value="empty_file5.mzid"/> 62 <element name="fraction_five_spectra" value="empty_file5.mzid"/>
63 <element name="fraction_six_spectra" value="empty_file6.mzid"/> 63 <element name="fraction_six_spectra" value="empty_file6.mzid"/>
68 <element name="fraction_eleven_spectra" value="empty_file11.mzid"/> 68 <element name="fraction_eleven_spectra" value="empty_file11.mzid"/>
69 </collection> 69 </collection>
70 </param> 70 </param>
71 <output_collection name="batched_fractions_mzid" type="list:list"> 71 <output_collection name="batched_fractions_mzid" type="list:list">
72 <element name="pool0_batch0"> 72 <element name="pool0_batch0">
73 <element name="inputfn00_fraction_one_spectra" ftype="mzid" file="empty_file1.mzid"/> 73 <element name="inputfn00_fraction_one_spectra.mzML" ftype="mzid" file="empty_file1.mzid"/>
74 <element name="inputfn01_fraction_two_spectra" ftype="mzid" file="empty_file2.mzid"/> 74 <element name="inputfn01_fraction_two_spectra" ftype="mzid" file="empty_file2.mzid"/>
75 <element name="inputfn02_fraction_three_spectra" ftype="mzid" file="empty_file3.mzid"/> 75 <element name="inputfn02_fraction_three_spectra" ftype="mzid" file="empty_file3.mzid"/>
76 <element name="inputfn03_fraction_four_spectra" ftype="mzid" file="empty_file4.mzid"/> 76 <element name="inputfn03_fraction_four_spectra" ftype="mzid" file="empty_file4.mzid"/>
77 <element name="inputfn04_fraction_five_spectra" ftype="mzid" file="empty_file5.mzid"/> 77 <element name="inputfn04_fraction_five_spectra" ftype="mzid" file="empty_file5.mzid"/>
78 <element name="inputfn05_fraction_six_spectra" ftype="mzid" file="empty_file6.mzid"/> 78 <element name="inputfn05_fraction_six_spectra" ftype="mzid" file="empty_file6.mzid"/>
94 <param name="pool_identifier" value="set2"/> 94 <param name="pool_identifier" value="set2"/>
95 </repeat> 95 </repeat>
96 <param name="filetype" value="tabular" /> 96 <param name="filetype" value="tabular" />
97 <param name="listtobatch"> 97 <param name="listtobatch">
98 <collection type="list"> 98 <collection type="list">
99 <element name="fr_one_set1_spectra" value="empty_file1.mzid"/> 99 <element name="fr_one_set1-spectra" value="empty_file1.mzid"/>
100 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/> 100 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/>
101 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/> 101 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/>
102 <element name="fr_four_set1_spectra" value="empty_file4.mzid"/> 102 <element name="fr_four_set1_spectra" value="empty_file4.mzid"/>
103 <element name="fr_five_set1_spectra" value="empty_file5.mzid"/> 103 <element name="fr_five_set1_spectra" value="empty_file5.mzid"/>
104 <element name="fr_six_set1_spectra" value="empty_file6.mzid"/> 104 <element name="fr_six_set1_spectra" value="empty_file6.mzid"/>
112 <element name="fr_three_set2_spectra" value="empty_file14.mzid"/> 112 <element name="fr_three_set2_spectra" value="empty_file14.mzid"/>
113 </collection> 113 </collection>
114 </param> 114 </param>
115 <output_collection name="batched_fractions_tab" type="list:list"> 115 <output_collection name="batched_fractions_tab" type="list:list">
116 <element name="set1_batch0"> 116 <element name="set1_batch0">
117 <element name="inputfn00_fr_one_set1_spectra" ftype="tabular" file="empty_file1.mzid"/> 117 <element name="inputfn00_fr_one_set1-spectra" ftype="tabular" file="empty_file1.mzid"/>
118 <element name="inputfn01_fr_two_set1_spectra" ftype="tabular" file="empty_file2.mzid"/> 118 <element name="inputfn01_fr_two_set1_spectra" ftype="tabular" file="empty_file2.mzid"/>
119 <element name="inputfn02_fr_three_set1_spectra" ftype="tabular" file="empty_file3.mzid"/> 119 <element name="inputfn02_fr_three_set1_spectra" ftype="tabular" file="empty_file3.mzid"/>
120 <element name="inputfn03_fr_four_set1_spectra" ftype="tabular" file="empty_file4.mzid"/> 120 <element name="inputfn03_fr_four_set1_spectra" ftype="tabular" file="empty_file4.mzid"/>
121 <element name="inputfn04_fr_five_set1_spectra" ftype="tabular" file="empty_file5.mzid"/> 121 <element name="inputfn04_fr_five_set1_spectra" ftype="tabular" file="empty_file5.mzid"/>
122 <element name="inputfn05_fr_six_set1_spectra" ftype="tabular" file="empty_file6.mzid"/> 122 <element name="inputfn05_fr_six_set1_spectra" ftype="tabular" file="empty_file6.mzid"/>