Mercurial > repos > gbcs-embl-heidelberg > je_demultiplex
diff je-demultiplex.xml @ 7:8f16495dc5f2 draft
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 |
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--- a/je-demultiplex.xml Fri Sep 15 08:17:48 2017 -0400 +++ b/je-demultiplex.xml Mon Mar 05 07:12:52 2018 -0500 @@ -60,7 +60,8 @@ <param name="type" value="single"/> <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/> <param name="BARCODE_FILE" value="barcodes_SE.txt" ftype="tabular"/> - <output name="METRICS_FILE_NAME" file="summary_SE.txt" ftype="tabular" lines_diff="4"> + <output name="METRICS_FILE_NAME" file="summary_SE.txt" ftype="tabular" lines_diff="4"/> + <output name="DEMULTIPLEX_RESULTS" ftype="tabular"> <discovered_dataset designation="unassigned_1" file="unassigned_1_SE.txt" /> </output> </test> @@ -74,10 +75,12 @@ <param name="BM" value="BOTH"/> <param name="BRED" value="false"/> + <param name="COLLECT_OUTPUTS" value="false" /> <param name="barcode_list_type_con" value="text"/> <param name="barcode_text" value="sample1 CACTGT:GTATAG sample2 ATTCCG:TCCGTC sample3 GCTACC:TGGTCA sample4 CGAAAC:CACTGT"/> - <output name="METRICS_FILE_NAME" file="summary_PE.txt" ftype="tabular" lines_diff="4"> + <output name="METRICS_FILE_NAME" file="summary_PE.txt" ftype="tabular" lines_diff="4"/> + <output name="DEMULTIPLEX_RESULTS" ftype="tabular"> <discovered_dataset designation="unassigned_1" file="unassigned_1_PE.txt" /> <discovered_dataset designation="unassigned_2" file="unassigned_2_PE.txt" /> <discovered_dataset designation="sample4_CGAAACCACTGT_2" file="sample4_CGAAACCACTGT_2.txt"/> @@ -90,6 +93,33 @@ <discovered_dataset designation="sample1_CACTGTGTATAG_1" file="sample1_CACTGTGTATAG_1.txt"/> </output> </test> + <test> + <!-- Repeat of previous but with collection outputs --> + <param name="type" value="paired"/> + <param name="input_1" value="file_1_sequence.txt" ftype="fastqsanger"/> + <param name="input_2" value="file_2_sequence.txt" ftype="fastqsanger"/> + + <param name="BPOS" value="BOTH"/> + <param name="BM" value="BOTH"/> + <param name="BRED" value="false"/> + <param name="barcode_list_type_con" value="text"/> + <param name="barcode_text" + value="sample1 CACTGT:GTATAG sample2 ATTCCG:TCCGTC sample3 GCTACC:TGGTCA sample4 CGAAAC:CACTGT"/> + <param name="COLLECT_OUTPUTS" value="true" /> + + <output_collection name="COLLECTION_1" type="list"> + <element name="sample1_CACTGTGTATAG_1.txt" value="sample4_CGAAACCACTGT_1.txt"/> + <element name="sample3_GCTACCTGGTCA_1.txt" value="sample3_GCTACCTGGTCA_1.txt"/> + <element name="sample2_ATTCCGTCCGTC_1.txt" value="sample2_ATTCCGTCCGTC_1.txt"/> + <element name="sample1_CACTGTGTATAG_1.txt" value="sample1_CACTGTGTATAG_1.txt"/> + </output_collection> + <output_collection name="COLLECTION_2" type="list"> + <element name="sample4_CGAAACCACTGT_2.txt" value="sample4_CGAAACCACTGT_2.txt"/> + <element name="sample3_GCTACCTGGTCA_2.txt" value="sample3_GCTACCTGGTCA_2.txt"/> + <element name="sample2_ATTCCGTCCGTC_2.txt" value="sample2_ATTCCGTCCGTC_2.txt"/> + <element name="sample1_CACTGTGTATAG_2.txt" value="sample1_CACTGTGTATAG_2.txt"/> + </output_collection> + </test> </tests> <help> @@ -104,6 +134,8 @@ Wrapper by: Jelle Scholtalbers (jelle.scholtalbers@embl.de). +With contributions by: Mehmet Tekman (@mtekman) + ------ **Know what you are doing**