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comparison nested_collection.xml @ 2:b20ea66c01f0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 4ca7fcd1587c906db3314048a223d23b63b3f038
author galaxyp
date Fri, 10 Mar 2017 03:20:38 -0500
parents 23141085ca9e
children d4b3842dc781
comparison
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1:23141085ca9e 2:b20ea66c01f0
1 <tool id="batched_set_list_creator" name="Create nested list" version="3.0.1"> 1 <tool id="batched_set_list_creator" name="Create nested list" version="3.1">
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
30 </repeat> 30 </repeat>
31 <param name="listtobatch" type="data_collection" collection_type="list" label="List of files to batch" /> 31 <param name="listtobatch" type="data_collection" collection_type="list" label="List of files to batch" />
32 </inputs> 32 </inputs>
33 <outputs> 33 <outputs>
34 <collection name="batched_fractions" type="list:list" label="Pooled batched data"> 34 <collection name="batched_fractions" type="list:list" label="Pooled batched data">
35 <discover_datasets pattern="[a-zA-z0-9_]*___(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;identifier_1&gt;[^_]+)\.mzid" ext="mzid" visible="true" /> 35 <discover_datasets pattern="(?P&lt;identifier_0&gt;\w+[^_][^_][^_])___(?P&lt;identifier_1&gt;[^_]+)\.mzid" ext="mzid" visible="true" />
36 </collection> 36 </collection>
37 </outputs> 37 </outputs>
38 <tests> 38 <tests>
39 <test> 39 <test>
40 <param name="batchsize" value="2"/> 40 <param name="batchsize" value="2"/>
45 <element name="fraction_three_spectra" value="empty_file3.mzid"/> 45 <element name="fraction_three_spectra" value="empty_file3.mzid"/>
46 <element name="fraction_four_spectra" value="empty_file4.mzid"/> 46 <element name="fraction_four_spectra" value="empty_file4.mzid"/>
47 </collection> 47 </collection>
48 </param> 48 </param>
49 <output_collection name="batched_fractions" type="list:list"> 49 <output_collection name="batched_fractions" type="list:list">
50 <element name="batch0"> 50 <element name="pool0_batch0">
51 <element name="inputfn0" file="empty_file1.mzid"/> 51 <element name="inputfn0" file="empty_file1.mzid"/>
52 <element name="inputfn1" file="empty_file2.mzid"/> 52 <element name="inputfn1" file="empty_file2.mzid"/>
53 </element> 53 </element>
54 <element name="batch1"> 54 <element name="pool0_batch1">
55 <element name="inputfn0" file="empty_file3.mzid"/> 55 <element name="inputfn0" file="empty_file3.mzid"/>
56 <element name="inputfn1" file="empty_file4.mzid"/> 56 <element name="inputfn1" file="empty_file4.mzid"/>
57 </element> 57 </element>
58 </output_collection> 58 </output_collection>
59 </test> 59 </test>
73 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/> 73 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
74 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/> 74 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
75 </collection> 75 </collection>
76 </param> 76 </param>
77 <output_collection name="batched_fractions" type="list:list"> 77 <output_collection name="batched_fractions" type="list:list">
78 <element name="batch0"> 78 <element name="set1_batch0">
79 <element name="inputfn0" file="empty_file1.mzid"/> 79 <element name="inputfn0" file="empty_file1.mzid"/>
80 <element name="inputfn1" file="empty_file2.mzid"/> 80 <element name="inputfn1" file="empty_file2.mzid"/>
81 <element name="inputfn2" file="empty_file3.mzid"/> 81 <element name="inputfn2" file="empty_file3.mzid"/>
82 </element> 82 </element>
83 <element name="batch1"> 83 <element name="set2_batch1">
84 <element name="inputfn0" file="empty_file4.mzid"/> 84 <element name="inputfn0" file="empty_file4.mzid"/>
85 <element name="inputfn1" file="empty_file5.mzid"/> 85 <element name="inputfn1" file="empty_file5.mzid"/>
86 <element name="inputfn2" file="empty_file6.mzid"/> 86 <element name="inputfn2" file="empty_file6.mzid"/>
87 </element> 87 </element>
88 </output_collection> 88 </output_collection>
104 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/> 104 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
105 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/> 105 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
106 </collection> 106 </collection>
107 </param> 107 </param>
108 <output_collection name="batched_fractions" type="list:list"> 108 <output_collection name="batched_fractions" type="list:list">
109 <element name="batch0"> 109 <element name="set1_batch0">
110 <element name="inputfn0" file="empty_file1.mzid"/> 110 <element name="inputfn0" file="empty_file1.mzid"/>
111 <element name="inputfn1" file="empty_file2.mzid"/> 111 <element name="inputfn1" file="empty_file2.mzid"/>
112 </element> 112 </element>
113 <element name="batch1"> 113 <element name="set1_batch1">
114 <element name="inputfn0" file="empty_file3.mzid"/> 114 <element name="inputfn0" file="empty_file3.mzid"/>
115 </element> 115 </element>
116 <element name="batch2"> 116 <element name="set2_batch2">
117 <element name="inputfn0" file="empty_file4.mzid"/> 117 <element name="inputfn0" file="empty_file4.mzid"/>
118 <element name="inputfn1" file="empty_file5.mzid"/> 118 <element name="inputfn1" file="empty_file5.mzid"/>
119 </element> 119 </element>
120 <element name="batch3"> 120 <element name="set2_batch3">
121 <element name="inputfn0" file="empty_file6.mzid"/> 121 <element name="inputfn0" file="empty_file6.mzid"/>
122 </element> 122 </element>
123 </output_collection> 123 </output_collection>
124 </test> 124 </test>
125 </tests> 125 </tests>