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comparison nested_collection.xml @ 4:154147805a33 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/percolator commit 9db2c1bb610ff3a6940f0a037c0fccf337692c36
author galaxyp
date Fri, 28 Apr 2017 12:25:36 -0400
parents abed51712ed0
children dce55ca21b98
comparison
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3:abed51712ed0 4:154147805a33
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;[^_]+)\.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;[^_]+)\.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;[^_]+)\.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="2"/> 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"/>
63 <element name="fraction_six_spectra" value="empty_file6.mzid"/>
64 <element name="fraction_seven_spectra" value="empty_file7.mzid"/>
65 <element name="fraction_eight_spectra" value="empty_file8.mzid"/>
66 <element name="fraction_nine_spectra" value="empty_file9.mzid"/>
67 <element name="fraction_ten_spectra" value="empty_file10.mzid"/>
68 <element name="fraction_eleven_spectra" value="empty_file11.mzid"/>
62 </collection> 69 </collection>
63 </param> 70 </param>
64 <output_collection name="batched_fractions_mzid" type="list:list"> 71 <output_collection name="batched_fractions_mzid" type="list:list">
65 <element name="pool0_batch0"> 72 <element name="pool0_batch0">
66 <element name="inputfn0" ftype="mzid" file="empty_file1.mzid"/> 73 <element name="inputfn00_fraction_one_spectra.mzML" ftype="mzid" file="empty_file1.mzid"/>
67 <element name="inputfn1" 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"/>
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"/>
78 <element name="inputfn05_fraction_six_spectra" ftype="mzid" file="empty_file6.mzid"/>
68 </element> 79 </element>
69 <element name="pool0_batch1"> 80 <element name="pool0_batch1">
70 <element name="inputfn0" ftype="mzid" file="empty_file3.mzid"/> 81 <element name="inputfn06_fraction_seven_spectra" ftype="mzid" file="empty_file7.mzid"/>
71 <element name="inputfn1" ftype="mzid" file="empty_file4.mzid"/> 82 <element name="inputfn07_fraction_eight_spectra" ftype="mzid" file="empty_file8.mzid"/>
83 <element name="inputfn08_fraction_nine_spectra" ftype="mzid" file="empty_file9.mzid"/>
84 <element name="inputfn09_fraction_ten_spectra" ftype="mzid" file="empty_file10.mzid"/>
85 <element name="inputfn10_fraction_eleven_spectra" ftype="mzid" file="empty_file10.mzid"/>
72 </element> 86 </element>
73 </output_collection> 87 </output_collection>
74 </test> 88 </test>
75 <test> 89 <test>
76 <repeat name="poolids"> 90 <repeat name="poolids">
83 <param name="listtobatch"> 97 <param name="listtobatch">
84 <collection type="list"> 98 <collection type="list">
85 <element name="fr_one_set1_spectra" value="empty_file1.mzid"/> 99 <element name="fr_one_set1_spectra" value="empty_file1.mzid"/>
86 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/> 100 <element name="fr_two_set1_spectra" value="empty_file2.mzid"/>
87 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/> 101 <element name="fr_three_set1_spectra" value="empty_file3.mzid"/>
88 <element name="fr_one_set2_spectra" value="empty_file4.mzid"/> 102 <element name="fr_four_set1_spectra" value="empty_file4.mzid"/>
89 <element name="fr_two_set2_spectra" value="empty_file5.mzid"/> 103 <element name="fr_five_set1_spectra" value="empty_file5.mzid"/>
90 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/> 104 <element name="fr_six_set1_spectra" value="empty_file6.mzid"/>
105 <element name="fr_seven_set1_spectra" value="empty_file7.mzid"/>
106 <element name="fr_eight_set1_spectra" value="empty_file8.mzid"/>
107 <element name="fr_nine_set1_spectra" value="empty_file9.mzid"/>
108 <element name="fr_ten_set1_spectra" value="empty_file10.mzid"/>
109 <element name="fr_eleven_set1_spectra" value="empty_file11.mzid"/>
110 <element name="fr_one_set2_spectra" value="empty_file12.mzid"/>
111 <element name="fr_two_set2_spectra" value="empty_file13.mzid"/>
112 <element name="fr_three_set2_spectra" value="empty_file14.mzid"/>
91 </collection> 113 </collection>
92 </param> 114 </param>
93 <output_collection name="batched_fractions_tab" type="list:list"> 115 <output_collection name="batched_fractions_tab" type="list:list">
94 <element name="set1_batch0"> 116 <element name="set1_batch0">
95 <element name="inputfn0" ftype="tabular" file="empty_file1.mzid"/> 117 <element name="inputfn00_fr_one_set1_spectra" ftype="tabular" file="empty_file1.mzid"/>
96 <element name="inputfn1" ftype="tabular" file="empty_file2.mzid"/> 118 <element name="inputfn01_fr_two_set1_spectra" ftype="tabular" file="empty_file2.mzid"/>
97 <element name="inputfn2" 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"/>
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"/>
123 <element name="inputfn06_fr_seven_set1_spectra" ftype="tabular" file="empty_file7.mzid"/>
124 <element name="inputfn07_fr_eight_set1_spectra" ftype="tabular" file="empty_file8.mzid"/>
125 <element name="inputfn08_fr_nine_set1_spectra" ftype="tabular" file="empty_file9.mzid"/>
126 <element name="inputfn09_fr_ten_set1_spectra" ftype="tabular" file="empty_file10.mzid"/>
127 <element name="inputfn10_fr_eleven_set1_spectra" ftype="tabular" file="empty_file11.mzid"/>
98 </element> 128 </element>
99 <element name="set2_batch1"> 129 <element name="set2_batch1">
100 <element name="inputfn0" ftype="tabular" file="empty_file4.mzid"/> 130 <element name="inputfn0_fr_one_set2_spectra" ftype="tabular" file="empty_file12.mzid"/>
101 <element name="inputfn1" ftype="tabular" file="empty_file5.mzid"/> 131 <element name="inputfn1_fr_two_set2_spectra" ftype="tabular" file="empty_file13.mzid"/>
102 <element name="inputfn2" ftype="tabular" file="empty_file6.mzid"/> 132 <element name="inputfn2_fr_three_set2_spectra" ftype="tabular" file="empty_file14.mzid"/>
103 </element> 133 </element>
104 </output_collection> 134 </output_collection>
105 </test> 135 </test>
106 <test> 136 <test>
107 <param name="batchsize" value="2"/> 137 <param name="batchsize" value="2"/>
122 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/> 152 <element name="fr_three_set2_spectra" value="empty_file6.mzid"/>
123 </collection> 153 </collection>
124 </param> 154 </param>
125 <output_collection name="batched_fractions_perco" type="list:list"> 155 <output_collection name="batched_fractions_perco" type="list:list">
126 <element name="set1_batch0"> 156 <element name="set1_batch0">
127 <element name="inputfn0" ftype="percout" file="empty_file1.mzid"/> 157 <element name="inputfn0_fr_one_set1_spectra" ftype="percout" file="empty_file1.mzid"/>
128 <element name="inputfn1" ftype="percout" file="empty_file2.mzid"/> 158 <element name="inputfn1_fr_two_set1_spectra" ftype="percout" file="empty_file2.mzid"/>
129 </element> 159 </element>
130 <element name="set1_batch1"> 160 <element name="set1_batch1">
131 <element name="inputfn0" ftype="percout" file="empty_file3.mzid"/> 161 <element name="inputfn2_fr_three_set1_spectra" ftype="percout" file="empty_file3.mzid"/>
132 </element> 162 </element>
133 <element name="set2_batch2"> 163 <element name="set2_batch2">
134 <element name="inputfn0" ftype="percout" file="empty_file4.mzid"/> 164 <element name="inputfn0_fr_one_set2_spectra" ftype="percout" file="empty_file4.mzid"/>
135 <element name="inputfn1" ftype="percout" file="empty_file5.mzid"/> 165 <element name="inputfn1_fr_two_set2_spectra" ftype="percout" file="empty_file5.mzid"/>
136 </element> 166 </element>
137 <element name="set2_batch3"> 167 <element name="set2_batch3">
138 <element name="inputfn0" ftype="percout" file="empty_file6.mzid"/> 168 <element name="inputfn2_fr_three_set2_spectra" ftype="percout" file="empty_file6.mzid"/>
139 </element> 169 </element>
140 </output_collection> 170 </output_collection>
141 </test> 171 </test>
142 </tests> 172 </tests>
143 <help> 173 <help>