Mercurial > repos > iuc > schicexplorer_schicdemultiplex
diff scHicDemultiplex.xml @ 1:649c86cedcb4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
| author | iuc |
|---|---|
| date | Tue, 10 Mar 2020 15:07:38 -0400 |
| parents | e59d83af97a1 |
| children | f224fc9af1d3 |
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--- a/scHicDemultiplex.xml Thu Jan 23 15:59:42 2020 -0500 +++ b/scHicDemultiplex.xml Tue Mar 10 15:07:38 2020 -0400 @@ -19,6 +19,12 @@ --bufferSize $bufferSize --threads @THREADS@ + && cd outputFiles + && mkdir forward + && mkdir reverse + && mv *R1.fastq.gz forward + && mv *R2.fastq.gz reverse + ]]></command> <inputs> @@ -29,8 +35,11 @@ </inputs> <outputs> - <collection name="outputFastqs" type="list" label="Demultiplexed fastq files"> - <discover_datasets pattern="__name__" format="fastq.gz" directory="outputFiles" /> + <collection name="outputFastqsForward" type="list" label="Demultiplexed fastq files: Forward"> + <discover_datasets pattern="__name__" format="fastqsanger.gz" directory="outputFiles/forward" /> + </collection> + <collection name="outputFastqsReverse" type="list" label="Demultiplexed fastq files: Reverse"> + <discover_datasets pattern="__name__" format="fastqsanger.gz" directory="outputFiles/reverse" /> </collection> </outputs> <tests> @@ -39,57 +48,60 @@ <param name='barcodeFile' value='scHicDemultiplex/GSE94489_README.txt' /> <param name='srrToSample' value='scHicDemultiplex/samples.txt' /> <param name='bufferSize' value='1000' /> + <output_collection name="outputFastqsForward" type="list" count="24"> + <!-- <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> --> + <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_15_CGTACTAG_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_CGTACTAG_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <!-- <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> --> + <element name="Diploid_15_GGACTCCT_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_GGACTCCT_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_15_TAAGGCGA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAAGGCGA_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_15_TAGGCATG_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAGGCATG_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_15_TCCTGAGC_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TCCTGAGC_CTCTCTAT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_16_AGGCAGAA_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_AGGCAGAA_TATCCTCT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_16_CGTACTAG_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_CGTACTAG_TATCCTCT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_16_GGACTCCT_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_GGACTCCT_TATCCTCT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_16_TAAGGCGA_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAAGGCGA_TATCCTCT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_16_TAGGCATG_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAGGCATG_TATCCTCT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_16_TCCTGAGC_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TCCTGAGC_TATCCTCT_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_17_AGGCAGAA_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_AGGCAGAA_GTAAGGAG_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_17_CGTACTAG_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_CGTACTAG_GTAAGGAG_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_17_GGACTCCT_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_GGACTCCT_GTAAGGAG_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_17_TAAGGCGA_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAAGGCGA_GTAAGGAG_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_17_TAGGCATG_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAGGCATG_GTAAGGAG_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_17_TCCTGAGC_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TCCTGAGC_GTAAGGAG_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_18_AGGCAGAA_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_AGGCAGAA_ACTGCATA_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_18_CGTACTAG_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_CGTACTAG_ACTGCATA_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_18_GGACTCCT_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_GGACTCCT_ACTGCATA_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_18_TAAGGCGA_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAAGGCGA_ACTGCATA_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_18_TAGGCATG_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAGGCATG_ACTGCATA_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_18_TCCTGAGC_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TCCTGAGC_ACTGCATA_R1.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + </output_collection> - - <output_collection name="outputFastqs" type="list" count="48"> - <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_15_CGTACTAG_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_CGTACTAG_CTCTCTAT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_15_CGTACTAG_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_CGTACTAG_CTCTCTAT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_15_GGACTCCT_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_GGACTCCT_CTCTCTAT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_15_GGACTCCT_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_GGACTCCT_CTCTCTAT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_15_TAAGGCGA_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAAGGCGA_CTCTCTAT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_15_TAAGGCGA_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAAGGCGA_CTCTCTAT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_15_TAGGCATG_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAGGCATG_CTCTCTAT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_15_TAGGCATG_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAGGCATG_CTCTCTAT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_15_TCCTGAGC_CTCTCTAT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TCCTGAGC_CTCTCTAT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_15_TCCTGAGC_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TCCTGAGC_CTCTCTAT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_16_AGGCAGAA_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_AGGCAGAA_TATCCTCT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_16_AGGCAGAA_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_AGGCAGAA_TATCCTCT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_16_CGTACTAG_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_CGTACTAG_TATCCTCT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_16_CGTACTAG_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_CGTACTAG_TATCCTCT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_16_GGACTCCT_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_GGACTCCT_TATCCTCT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_16_GGACTCCT_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_GGACTCCT_TATCCTCT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_16_TAAGGCGA_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAAGGCGA_TATCCTCT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_16_TAAGGCGA_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAAGGCGA_TATCCTCT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_16_TAGGCATG_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAGGCATG_TATCCTCT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_16_TAGGCATG_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAGGCATG_TATCCTCT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_16_TCCTGAGC_TATCCTCT_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TCCTGAGC_TATCCTCT_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_16_TCCTGAGC_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TCCTGAGC_TATCCTCT_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_17_AGGCAGAA_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_AGGCAGAA_GTAAGGAG_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_17_AGGCAGAA_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_AGGCAGAA_GTAAGGAG_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_17_CGTACTAG_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_CGTACTAG_GTAAGGAG_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_17_CGTACTAG_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_CGTACTAG_GTAAGGAG_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_17_GGACTCCT_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_GGACTCCT_GTAAGGAG_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_17_GGACTCCT_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_GGACTCCT_GTAAGGAG_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_17_TAAGGCGA_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAAGGCGA_GTAAGGAG_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_17_TAAGGCGA_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAAGGCGA_GTAAGGAG_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_17_TAGGCATG_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAGGCATG_GTAAGGAG_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_17_TAGGCATG_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAGGCATG_GTAAGGAG_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_17_TCCTGAGC_GTAAGGAG_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TCCTGAGC_GTAAGGAG_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_17_TCCTGAGC_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TCCTGAGC_GTAAGGAG_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_18_AGGCAGAA_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_AGGCAGAA_ACTGCATA_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_18_AGGCAGAA_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_AGGCAGAA_ACTGCATA_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_18_CGTACTAG_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_CGTACTAG_ACTGCATA_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_18_CGTACTAG_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_CGTACTAG_ACTGCATA_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_18_GGACTCCT_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_GGACTCCT_ACTGCATA_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_18_GGACTCCT_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_GGACTCCT_ACTGCATA_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_18_TAAGGCGA_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAAGGCGA_ACTGCATA_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_18_TAAGGCGA_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAAGGCGA_ACTGCATA_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_18_TAGGCATG_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAGGCATG_ACTGCATA_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_18_TAGGCATG_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAGGCATG_ACTGCATA_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_18_TCCTGAGC_ACTGCATA_R1.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TCCTGAGC_ACTGCATA_R1.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> - <element name="Diploid_18_TCCTGAGC_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TCCTGAGC_ACTGCATA_R2.fastq.gz" ftype="fastq.gz" compare='sim_size' delta='40000'/> + <output_collection name="outputFastqsReverse" type="list" count="24"> + <element name="Diploid_15_AGGCAGAA_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_AGGCAGAA_CTCTCTAT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_15_CGTACTAG_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_CGTACTAG_CTCTCTAT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_15_GGACTCCT_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_GGACTCCT_CTCTCTAT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_15_TAAGGCGA_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAAGGCGA_CTCTCTAT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_15_TAGGCATG_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TAGGCATG_CTCTCTAT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_15_TCCTGAGC_CTCTCTAT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_15_TCCTGAGC_CTCTCTAT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_16_AGGCAGAA_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_AGGCAGAA_TATCCTCT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_16_CGTACTAG_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_CGTACTAG_TATCCTCT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_16_GGACTCCT_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_GGACTCCT_TATCCTCT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_16_TAAGGCGA_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAAGGCGA_TATCCTCT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_16_TAGGCATG_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TAGGCATG_TATCCTCT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_16_TCCTGAGC_TATCCTCT_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_16_TCCTGAGC_TATCCTCT_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_17_AGGCAGAA_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_AGGCAGAA_GTAAGGAG_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_17_CGTACTAG_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_CGTACTAG_GTAAGGAG_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_17_GGACTCCT_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_GGACTCCT_GTAAGGAG_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_17_TAAGGCGA_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAAGGCGA_GTAAGGAG_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_17_TAGGCATG_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TAGGCATG_GTAAGGAG_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_17_TCCTGAGC_GTAAGGAG_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_17_TCCTGAGC_GTAAGGAG_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_18_AGGCAGAA_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_AGGCAGAA_ACTGCATA_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_18_CGTACTAG_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_CGTACTAG_ACTGCATA_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_18_GGACTCCT_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_GGACTCCT_ACTGCATA_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_18_TAAGGCGA_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAAGGCGA_ACTGCATA_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_18_TAGGCATG_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TAGGCATG_ACTGCATA_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> + <element name="Diploid_18_TCCTGAGC_ACTGCATA_R2.fastq.gz" file="scHicDemultiplex/demultiplexed/Diploid_18_TCCTGAGC_ACTGCATA_R2.fastq.gz" ftype="fastqsanger.gz" compare='sim_size' delta='40000'/> </output_collection> </test> </tests> @@ -99,7 +111,9 @@ ================================= scHicDemultiplex demultiplexes fastq files from Nagano 2017: "Cell-cycle dynamics of chromosomal organization at single-cell resolution" according their barcodes to -a seperated forward and reverse strand fastq files per cell. +a seperated forward and reverse strand fastq files per cell. For other datasets, a third-party demultiplexing strategy must be used. + +Afterwards, the demultiplexed mapped data can be used with HiCExplorer `hicBuildMatrix` to create single cell .cool matrices that must be stored in a .scool file using `scHicMergeToSCool`, in order to be used for downstream analyses in the scHiCExplorer suite. For more information about scHiCExplorer please consider our documentation on readthedocs.io_