Mercurial > repos > gbcs-embl-heidelberg > je_demultiplex

comparison je-demultiplex.xml @ 7:8f16495dc5f2 draft

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planemo upload for repository https://git.embl.de/grp-gbcs/Je/tree/master/src/galaxy commit e217faa15f73427979bb212036cb130a14c59750
author gbcs-embl-heidelberg
date Mon, 05 Mar 2018 07:12:52 -0500
parents 222819c87d90
children
comparison
equal deleted inserted replaced
6:dacd089d81ae 7:8f16495dc5f2
58 <test> 58 <test>
59 <!-- simple test on single end data --> 59 <!-- simple test on single end data -->
60 <param name="type" value="single"/> 60 <param name="type" value="single"/>
61 <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/> 61 <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/>
62 <param name="BARCODE_FILE" value="barcodes_SE.txt" ftype="tabular"/> 62 <param name="BARCODE_FILE" value="barcodes_SE.txt" ftype="tabular"/>
63 <output name="METRICS_FILE_NAME" file="summary_SE.txt" ftype="tabular" lines_diff="4"> 63 <output name="METRICS_FILE_NAME" file="summary_SE.txt" ftype="tabular" lines_diff="4"/>
64 <output name="DEMULTIPLEX_RESULTS" ftype="tabular">
64 <discovered_dataset designation="unassigned_1" file="unassigned_1_SE.txt" /> 65 <discovered_dataset designation="unassigned_1" file="unassigned_1_SE.txt" />
65 </output> 66 </output>
66 </test> 67 </test>
67 <test> 68 <test>
68 <!-- more complex test on paired end data with different barcode for fwd/rev --> 69 <!-- more complex test on paired end data with different barcode for fwd/rev -->
72 73
73 <param name="BPOS" value="BOTH"/> 74 <param name="BPOS" value="BOTH"/>
74 <param name="BM" value="BOTH"/> 75 <param name="BM" value="BOTH"/>
75 <param name="BRED" value="false"/> 76 <param name="BRED" value="false"/>
76 77
78 <param name="COLLECT_OUTPUTS" value="false" />
77 <param name="barcode_list_type_con" value="text"/> 79 <param name="barcode_list_type_con" value="text"/>
78 <param name="barcode_text" 80 <param name="barcode_text"
79 value="sample1 CACTGT:GTATAG&#10;sample2 ATTCCG:TCCGTC&#10;sample3 GCTACC:TGGTCA&#10;sample4 CGAAAC:CACTGT"/> 81 value="sample1 CACTGT:GTATAG&#10;sample2 ATTCCG:TCCGTC&#10;sample3 GCTACC:TGGTCA&#10;sample4 CGAAAC:CACTGT"/>
80 <output name="METRICS_FILE_NAME" file="summary_PE.txt" ftype="tabular" lines_diff="4"> 82 <output name="METRICS_FILE_NAME" file="summary_PE.txt" ftype="tabular" lines_diff="4"/>
83 <output name="DEMULTIPLEX_RESULTS" ftype="tabular">
81 <discovered_dataset designation="unassigned_1" file="unassigned_1_PE.txt" /> 84 <discovered_dataset designation="unassigned_1" file="unassigned_1_PE.txt" />
82 <discovered_dataset designation="unassigned_2" file="unassigned_2_PE.txt" /> 85 <discovered_dataset designation="unassigned_2" file="unassigned_2_PE.txt" />
83 <discovered_dataset designation="sample4_CGAAACCACTGT_2" file="sample4_CGAAACCACTGT_2.txt"/> 86 <discovered_dataset designation="sample4_CGAAACCACTGT_2" file="sample4_CGAAACCACTGT_2.txt"/>
84 <discovered_dataset designation="sample4_CGAAACCACTGT_1" file="sample4_CGAAACCACTGT_1.txt"/> 87 <discovered_dataset designation="sample4_CGAAACCACTGT_1" file="sample4_CGAAACCACTGT_1.txt"/>
85 <discovered_dataset designation="sample3_GCTACCTGGTCA_2" file="sample3_GCTACCTGGTCA_2.txt"/> 88 <discovered_dataset designation="sample3_GCTACCTGGTCA_2" file="sample3_GCTACCTGGTCA_2.txt"/>
88 <discovered_dataset designation="sample2_ATTCCGTCCGTC_1" file="sample2_ATTCCGTCCGTC_1.txt"/> 91 <discovered_dataset designation="sample2_ATTCCGTCCGTC_1" file="sample2_ATTCCGTCCGTC_1.txt"/>
89 <discovered_dataset designation="sample1_CACTGTGTATAG_2" file="sample1_CACTGTGTATAG_2.txt"/> 92 <discovered_dataset designation="sample1_CACTGTGTATAG_2" file="sample1_CACTGTGTATAG_2.txt"/>
90 <discovered_dataset designation="sample1_CACTGTGTATAG_1" file="sample1_CACTGTGTATAG_1.txt"/> 93 <discovered_dataset designation="sample1_CACTGTGTATAG_1" file="sample1_CACTGTGTATAG_1.txt"/>
91 </output> 94 </output>
92 </test> 95 </test>
96 <test>
97 <!-- Repeat of previous but with collection outputs -->
98 <param name="type" value="paired"/>
99 <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/>
100 <param name="input_2" value="file_2_sequence.txt" ftype="fastqsanger"/>
101
102 <param name="BPOS" value="BOTH"/>
103 <param name="BM" value="BOTH"/>
104 <param name="BRED" value="false"/>
105 <param name="barcode_list_type_con" value="text"/>
106 <param name="barcode_text"
107 value="sample1 CACTGT:GTATAG&#10;sample2 ATTCCG:TCCGTC&#10;sample3 GCTACC:TGGTCA&#10;sample4 CGAAAC:CACTGT"/>
108 <param name="COLLECT_OUTPUTS" value="true" />
109
110 <output_collection name="COLLECTION_1" type="list">
111 <element name="sample1_CACTGTGTATAG_1.txt" value="sample4_CGAAACCACTGT_1.txt"/>
112 <element name="sample3_GCTACCTGGTCA_1.txt" value="sample3_GCTACCTGGTCA_1.txt"/>
113 <element name="sample2_ATTCCGTCCGTC_1.txt" value="sample2_ATTCCGTCCGTC_1.txt"/>
114 <element name="sample1_CACTGTGTATAG_1.txt" value="sample1_CACTGTGTATAG_1.txt"/>
115 </output_collection>
116 <output_collection name="COLLECTION_2" type="list">
117 <element name="sample4_CGAAACCACTGT_2.txt" value="sample4_CGAAACCACTGT_2.txt"/>
118 <element name="sample3_GCTACCTGGTCA_2.txt" value="sample3_GCTACCTGGTCA_2.txt"/>
119 <element name="sample2_ATTCCGTCCGTC_2.txt" value="sample2_ATTCCGTCCGTC_2.txt"/>
120 <element name="sample1_CACTGTGTATAG_2.txt" value="sample1_CACTGTGTATAG_2.txt"/>
121 </output_collection>
122 </test>
93 </tests> 123 </tests>
94 124
95 <help> 125 <help>
96 <![CDATA[ 126 <![CDATA[
97 **What it does** 127 **What it does**
101 Input files are fastq files, and can be in gzip compressed format. 131 Input files are fastq files, and can be in gzip compressed format.
102 132
103 Author: Charles Girardot (charles.girardot@embl.de). 133 Author: Charles Girardot (charles.girardot@embl.de).
104 134
105 Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de). 135 Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de).
136
137 With contributions by: Mehmet Tekman (@mtekman)
106 138
107 ------ 139 ------
108 140
109 **Know what you are doing** 141 **Know what you are doing**
110 142