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comparison nested_collection.xml @ 3:abed51712ed0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit b3873302e7bb7917a43b455875208e6e9fcf8f66
author galaxyp
date Sat, 08 Apr 2017 08:23:12 -0400
parents 7a0951d0e13e
children 154147805a33
comparison
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2:7a0951d0e13e 3:abed51712ed0
1 <tool id="batched_set_list_creator" name="Create nested list" version="3.1"> 1 <tool id="batched_set_list_creator" name="Create nested list" version="3.2">
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 $__tool_directory__/nested_collection.py
22 '$listtobatch[$fname]' 22 '$listtobatch[$fname]'
23 #end for 23 #end for
24 </command> 24 </command>
25 <inputs> 25 <inputs>
26 <param name="batchsize" type="integer" optional="true" value="" label="Maximal amount of fractions to batch." help="No value means no maximum" /> 26 <param name="batchsize" type="integer" optional="true" value="" label="Maximal amount of fractions to batch." help="No value means no maximum" />
27 <param name="filetype" type="select" label="Which datatype to nest?">
28 <option value="mzid">mzIdentML</option>
29 <option value="percout">Percolator out</option>
30 <option value="tabular">Tabular</option>
31 </param>
27 <repeat name="poolids" title="Batch pools" help="Pools containing batches (optional, not using this will result in one pool)"> 32 <repeat name="poolids" title="Batch pools" help="Pools containing batches (optional, not using this will result in one pool)">
28 <param name="pool_identifier" type="text" label="Filename part identifying batchpool" 33 <param name="pool_identifier" type="text" label="Filename part identifying batchpool"
29 help="Specify part of the input filenames that are unique for each pool, e.g set_A. Do not use 3 consecutive underscores."/> 34 help="Specify part of the input filenames that are unique for each pool, e.g set_A. Do not use 3 consecutive underscores."/>
30 </repeat> 35 </repeat>
31 <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" />
32 </inputs> 37 </inputs>
33 <outputs> 38 <outputs>
34 <collection name="batched_fractions" type="list:list" label="Pooled batched data"> 39 <collection name="batched_fractions_mzid" type="list:list" label="Pooled batched mzIdentML data">
35 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[^_]+)\.mzid" ext="mzid" visible="true" /> 40 <filter>filetype == "mzid"</filter>
41 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[^_]+)\.data" ext="mzid" visible="false" />
42 </collection>
43 <collection name="batched_fractions_perco" type="list:list" label="Pooled batched percolator data">
44 <filter>filetype == "percout"</filter>
45 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[^_]+)\.data" ext="percout" visible="false" />
46 </collection>
47 <collection name="batched_fractions_tab" type="list:list" label="Pooled batched tabular data">
48 <filter>filetype == "tabular"</filter>
49 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[^_]+)\.data" ext="tabular" visible="false" />
36 </collection> 50 </collection>
37 </outputs> 51 </outputs>
38 <tests> 52 <tests>
39 <test> 53 <test>
40 <param name="batchsize" value="2"/> 54 <param name="batchsize" value="2"/>
55 <param name="filetype" value="mzid" />
41 <param name="listtobatch"> 56 <param name="listtobatch">
42 <collection type="list"> 57 <collection type="list">
43 <element name="fraction_one_spectra" value="empty_file1.mzid"/> 58 <element name="fraction_one_spectra" value="empty_file1.mzid"/>
44 <element name="fraction_two_spectra" value="empty_file2.mzid"/> 59 <element name="fraction_two_spectra" value="empty_file2.mzid"/>
45 <element name="fraction_three_spectra" value="empty_file3.mzid"/> 60 <element name="fraction_three_spectra" value="empty_file3.mzid"/>
46 <element name="fraction_four_spectra" value="empty_file4.mzid"/> 61 <element name="fraction_four_spectra" value="empty_file4.mzid"/>
47 </collection> 62 </collection>
48 </param> 63 </param>
49 <output_collection name="batched_fractions" type="list:list"> 64 <output_collection name="batched_fractions_mzid" type="list:list">
50 <element name="pool0_batch0"> 65 <element name="pool0_batch0">
51 <element name="inputfn0" file="empty_file1.mzid"/> 66 <element name="inputfn0" ftype="mzid" file="empty_file1.mzid"/>
52 <element name="inputfn1" file="empty_file2.mzid"/> 67 <element name="inputfn1" ftype="mzid" file="empty_file2.mzid"/>
53 </element> 68 </element>
54 <element name="pool0_batch1"> 69 <element name="pool0_batch1">
55 <element name="inputfn0" file="empty_file3.mzid"/> 70 <element name="inputfn0" ftype="mzid" file="empty_file3.mzid"/>
56 <element name="inputfn1" file="empty_file4.mzid"/> 71 <element name="inputfn1" ftype="mzid" file="empty_file4.mzid"/>
57 </element> 72 </element>
58 </output_collection> 73 </output_collection>
59 </test> 74 </test>
60 <test> 75 <test>
61 <repeat name="poolids"> 76 <repeat name="poolids">
62 <param name="pool_identifier" value="set1"/> 77 <param name="pool_identifier" value="set1"/>
63 </repeat> 78 </repeat>
64 <repeat name="poolids"> 79 <repeat name="poolids">
65 <param name="pool_identifier" value="set2"/> 80 <param name="pool_identifier" value="set2"/>
66 </repeat> 81 </repeat>
82 <param name="filetype" value="tabular" />
67 <param name="listtobatch"> 83 <param name="listtobatch">
68 <collection type="list"> 84 <collection type="list">
69 <element name="fr_one_set1_spectra" value="empty_file1.mzid"/> 85 <element name="fr_one_set1_spectra" value="empty_file1.mzid"/>
70 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/> 86 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/>
71 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/> 87 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/>
72 <element name="fr_one_set2_spectra" value="empty_file4.mzid"/> 88 <element name="fr_one_set2_spectra" value="empty_file4.mzid"/>
73 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/> 89 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
74 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/> 90 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
75 </collection> 91 </collection>
76 </param> 92 </param>
77 <output_collection name="batched_fractions" type="list:list"> 93 <output_collection name="batched_fractions_tab" type="list:list">
78 <element name="set1_batch0"> 94 <element name="set1_batch0">
79 <element name="inputfn0" file="empty_file1.mzid"/> 95 <element name="inputfn0" ftype="tabular" file="empty_file1.mzid"/>
80 <element name="inputfn1" file="empty_file2.mzid"/> 96 <element name="inputfn1" ftype="tabular" file="empty_file2.mzid"/>
81 <element name="inputfn2" file="empty_file3.mzid"/> 97 <element name="inputfn2" ftype="tabular" file="empty_file3.mzid"/>
82 </element> 98 </element>
83 <element name="set2_batch1"> 99 <element name="set2_batch1">
84 <element name="inputfn0" file="empty_file4.mzid"/> 100 <element name="inputfn0" ftype="tabular" file="empty_file4.mzid"/>
85 <element name="inputfn1" file="empty_file5.mzid"/> 101 <element name="inputfn1" ftype="tabular" file="empty_file5.mzid"/>
86 <element name="inputfn2" file="empty_file6.mzid"/> 102 <element name="inputfn2" ftype="tabular" file="empty_file6.mzid"/>
87 </element> 103 </element>
88 </output_collection> 104 </output_collection>
89 </test> 105 </test>
90 <test> 106 <test>
91 <param name="batchsize" value="2"/> 107 <param name="batchsize" value="2"/>
93 <param name="pool_identifier" value="set1"/> 109 <param name="pool_identifier" value="set1"/>
94 </repeat> 110 </repeat>
95 <repeat name="poolids"> 111 <repeat name="poolids">
96 <param name="pool_identifier" value="set2"/> 112 <param name="pool_identifier" value="set2"/>
97 </repeat> 113 </repeat>
114 <param name="filetype" value="percout" />
98 <param name="listtobatch"> 115 <param name="listtobatch">
99 <collection type="list"> 116 <collection type="list">
100 <element name="fr_one_set1_spectra" value="empty_file1.mzid"/> 117 <element name="fr_one_set1_spectra" value="empty_file1.mzid"/>
101 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/> 118 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/>
102 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/> 119 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/>
103 <element name="fr_one_set2_spectra" value="empty_file4.mzid"/> 120 <element name="fr_one_set2_spectra" value="empty_file4.mzid"/>
104 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/> 121 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
105 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/> 122 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
106 </collection> 123 </collection>
107 </param> 124 </param>
108 <output_collection name="batched_fractions" type="list:list"> 125 <output_collection name="batched_fractions_perco" type="list:list">
109 <element name="set1_batch0"> 126 <element name="set1_batch0">
110 <element name="inputfn0" file="empty_file1.mzid"/> 127 <element name="inputfn0" ftype="percout" file="empty_file1.mzid"/>
111 <element name="inputfn1" file="empty_file2.mzid"/> 128 <element name="inputfn1" ftype="percout" file="empty_file2.mzid"/>
112 </element> 129 </element>
113 <element name="set1_batch1"> 130 <element name="set1_batch1">
114 <element name="inputfn0" file="empty_file3.mzid"/> 131 <element name="inputfn0" ftype="percout" file="empty_file3.mzid"/>
115 </element> 132 </element>
116 <element name="set2_batch2"> 133 <element name="set2_batch2">
117 <element name="inputfn0" file="empty_file4.mzid"/> 134 <element name="inputfn0" ftype="percout" file="empty_file4.mzid"/>
118 <element name="inputfn1" file="empty_file5.mzid"/> 135 <element name="inputfn1" ftype="percout" file="empty_file5.mzid"/>
119 </element> 136 </element>
120 <element name="set2_batch3"> 137 <element name="set2_batch3">
121 <element name="inputfn0" file="empty_file6.mzid"/> 138 <element name="inputfn0" ftype="percout" file="empty_file6.mzid"/>
122 </element> 139 </element>
123 </output_collection> 140 </output_collection>
124 </test> 141 </test>
125 </tests> 142 </tests>
126 <help> 143 <help>