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comparison nested_collection.xml @ 1:86770eea5b09 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 0a5f9eb82877545be1c924357e585b17e01cfd1c
author galaxyp
date Sat, 04 Mar 2017 20:36:03 -0500
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children 7a0951d0e13e
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0:3a49065a05d6 1:86770eea5b09
1 <tool id="batched_set_list_creator" name="Create nested list" version="3.0.1">
2 <description>based on filenames and batch sizes</description>
3 <stdio>
4 <exit_code range="1:" />
5 </stdio>
6 <command>python $__tool_directory__/nested_collection.py
7 #if $batchsize
8 --batchsize $batchsize
9 #end if
10 #if len($poolids) > 0
11 --pool-ids
12 #for $pool in $poolids
13 '${pool.pool_identifier}'
14 #end for
15 #end if
16 --real-names
17 #for $fname in $listtobatch.keys()
18 '$fname'
19 #end for
20 --galaxy-files
21 #for $fname in $listtobatch.keys()
22 '$listtobatch[$fname]'
23 #end for
24 </command>
25 <inputs>
26 <param name="batchsize" type="integer" optional="true" value="" label="Maximal amount of fractions to batch." help="No value means no maximum" />
27 <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"
29 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>
31 <param name="listtobatch" type="data_collection" collection_type="list" label="List of files to batch" />
32 </inputs>
33 <outputs>
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" />
36 </collection>
37 </outputs>
38 <tests>
39 <test>
40 <param name="batchsize" value="2"/>
41 <param name="listtobatch">
42 <collection type="list">
43 <element name="fraction_one_spectra" value="empty_file1.mzid"/>
44 <element name="fraction_two_spectra" value="empty_file2.mzid"/>
45 <element name="fraction_three_spectra" value="empty_file3.mzid"/>
46 <element name="fraction_four_spectra" value="empty_file4.mzid"/>
47 </collection>
48 </param>
49 <output_collection name="batched_fractions" type="list:list">
50 <element name="batch0">
51 <element name="inputfn0" file="empty_file1.mzid"/>
52 <element name="inputfn1" file="empty_file2.mzid"/>
53 </element>
54 <element name="batch1">
55 <element name="inputfn0" file="empty_file3.mzid"/>
56 <element name="inputfn1" file="empty_file4.mzid"/>
57 </element>
58 </output_collection>
59 </test>
60 <test>
61 <repeat name="poolids">
62 <param name="pool_identifier" value="set1"/>
63 </repeat>
64 <repeat name="poolids">
65 <param name="pool_identifier" value="set2"/>
66 </repeat>
67 <param name="listtobatch">
68 <collection type="list">
69 <element name="fr_one_set1_spectra" value="empty_file1.mzid"/>
70 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/>
71 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/>
72 <element name="fr_one_set2_spectra" value="empty_file4.mzid"/>
73 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
74 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
75 </collection>
76 </param>
77 <output_collection name="batched_fractions" type="list:list">
78 <element name="batch0">
79 <element name="inputfn0" file="empty_file1.mzid"/>
80 <element name="inputfn1" file="empty_file2.mzid"/>
81 <element name="inputfn2" file="empty_file3.mzid"/>
82 </element>
83 <element name="batch1">
84 <element name="inputfn0" file="empty_file4.mzid"/>
85 <element name="inputfn1" file="empty_file5.mzid"/>
86 <element name="inputfn2" file="empty_file6.mzid"/>
87 </element>
88 </output_collection>
89 </test>
90 <test>
91 <param name="batchsize" value="2"/>
92 <repeat name="poolids">
93 <param name="pool_identifier" value="set1"/>
94 </repeat>
95 <repeat name="poolids">
96 <param name="pool_identifier" value="set2"/>
97 </repeat>
98 <param name="listtobatch">
99 <collection type="list">
100 <element name="fr_one_set1_spectra" value="empty_file1.mzid"/>
101 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/>
102 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/>
103 <element name="fr_one_set2_spectra" value="empty_file4.mzid"/>
104 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/>
105 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
106 </collection>
107 </param>
108 <output_collection name="batched_fractions" type="list:list">
109 <element name="batch0">
110 <element name="inputfn0" file="empty_file1.mzid"/>
111 <element name="inputfn1" file="empty_file2.mzid"/>
112 </element>
113 <element name="batch1">
114 <element name="inputfn0" file="empty_file3.mzid"/>
115 </element>
116 <element name="batch2">
117 <element name="inputfn0" file="empty_file4.mzid"/>
118 <element name="inputfn1" file="empty_file5.mzid"/>
119 </element>
120 <element name="batch3">
121 <element name="inputfn0" file="empty_file6.mzid"/>
122 </element>
123 </output_collection>
124 </test>
125 </tests>
126 <help>
127 Creates nested collection containing from a list containing datasets in batches of
128 a specific size. Useful when e.g. creating inputs to sqt2pin, msgfplus2pin or tandem2pin.
129 Use this feature when you want to batch a specific amount of datasets, or datasets with
130 a common file name pattern, or both.
131 The tool generates a collection containing batches which contain multiple batches
132 of input files. The pools are specified as a pattern in the input
133 files which makes sure the batching isn't continued through very different input sets
134 if that is a problem. Instead, for each filename-pattern it generates batches of the
135 specified size.
136 </help>
137 </tool>