Mercurial > repos > iuc > schicexplorer_schicdemultiplex
diff scHicDemultiplex.xml @ 0:e59d83af97a1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
| author | iuc |
|---|---|
| date | Thu, 23 Jan 2020 15:59:42 -0500 |
| parents | |
| children | 649c86cedcb4 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scHicDemultiplex.xml Thu Jan 23 15:59:42 2020 -0500 @@ -0,0 +1,110 @@ +<tool id="schicexplorer_schicdemultiplex" name="@BINARY@" version="@WRAPPER_VERSION@.0"> + <description>demultiplexes Nagano 2017 raw fastq files</description> + <macros> + <token name="@BINARY@">scHicDemultiplex</token> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + #import re + mkdir outputFiles && + #set fastqFile = @ESCAPE_IDENTIFIER_FASTQ@ + ln -s '$fastq' '$fastqFile' && + @BINARY@ + + --fastq $fastqFile + --barcodeFile '$barcodeFile' + --srrToSampleFile '$srrToSample' + --outputFolder outputFiles + --bufferSize $bufferSize + --threads @THREADS@ + + ]]></command> + <inputs> + + <param name='fastq' type="data" format="fastq, fastq.gz" label="Raw fastq file from Nagano 2017."/> + <param name='barcodeFile' type="data" format="txt" label="barcode file" help="Use GSE94489_README.txt file "/> + <param name='srrToSample' type="data" format="txt" label="SRR to Sample mapping file" help="The mappings from SRR number to sample id as given in the barcode file."/> + <param name="bufferSize" type="integer" value="20000000" label="Buffer size" help="Number of lines to buffer in memory, if full, write the data to disk." /> + + </inputs> + <outputs> + <collection name="outputFastqs" type="list" label="Demultiplexed fastq files"> + <discover_datasets pattern="__name__" format="fastq.gz" directory="outputFiles" /> + </collection> + </outputs> + <tests> + <test> + <param name='fastq' value='scHicDemultiplex/SRR5229025.fastq.gz' ftype="fastq.gz" /> + <param name='barcodeFile' value='scHicDemultiplex/GSE94489_README.txt' /> + <param name='srrToSample' value='scHicDemultiplex/samples.txt' /> + <param name='bufferSize' value='1000' /> + + + <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> + </test> + </tests> + <help><![CDATA[ + +Demultiplexing of raw fastq files +================================= + +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. + +For more information about scHiCExplorer please consider our documentation on readthedocs.io_ + +.. _readthedocs.io: http://schicexplorer.readthedocs.io/ +]]></help> + <expand macro="citations" /> + +</tool>