Mercurial > repos > iuc > schicexplorer_schicdemultiplex

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
author iuc
date Fri, 14 Apr 2023 14:20:29 +0000
parents 649c86cedcb4
children
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f224fc9af1d3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit d350f8e73ae518245a21f9720f8282f06eb9cc5d
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1 <tool id="schicexplorer_schicdemultiplex" name="@BINARY@" version="@TOOL_VERSION@.1" profile="@PROFILE@">
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2 <description>demultiplexes Nagano 2017 raw fastq files</description>
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3 <macros>
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4 <token name="@BINARY@">scHicDemultiplex</token>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import re
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10 mkdir outputFiles &&
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11 #set fastqFile = @ESCAPE_IDENTIFIER_FASTQ@
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12 ln -s '$fastq' '$fastqFile' &&
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13 @BINARY@
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14
e59d83af97a1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 2a80f777c0221752232882c0d43b55f2b1dcd223"
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15 --fastq $fastqFile
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16 --barcodeFile '$barcodeFile'
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17 --srrToSampleFile '$srrToSample'
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18 --outputFolder outputFiles
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19 --bufferSize $bufferSize
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20 --threads @THREADS@
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21
1
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22 && cd outputFiles
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23 && mkdir forward
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24 && mkdir reverse
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25 && mv *R1.fastq.gz forward
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26 && mv *R2.fastq.gz reverse
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27
0
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28 ]]></command>
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29 <inputs>
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30
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31 <param name='fastq' type="data" format="fastq, fastq.gz" label="Raw fastq file from Nagano 2017."/>
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32 <param name='barcodeFile' type="data" format="txt" label="barcode file" help="Use GSE94489_README.txt file "/>
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33 <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."/>
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34 <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." />
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35
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36 </inputs>
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37 <outputs>
1
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38 <collection name="outputFastqsForward" type="list" label="Demultiplexed fastq files: Forward">
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39 <discover_datasets pattern="__name__" format="fastqsanger.gz" directory="outputFiles/forward" />
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40 </collection>
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41 <collection name="outputFastqsReverse" type="list" label="Demultiplexed fastq files: Reverse">
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42 <discover_datasets pattern="__name__" format="fastqsanger.gz" directory="outputFiles/reverse" />
0
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43 </collection>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name='fastq' value='scHicDemultiplex/SRR5229025.fastq.gz' ftype="fastq.gz" />
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48 <param name='barcodeFile' value='scHicDemultiplex/GSE94489_README.txt' />
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49 <param name='srrToSample' value='scHicDemultiplex/samples.txt' />
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50 <param name='bufferSize' value='1000' />
1
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51 <output_collection name="outputFastqsForward" type="list" count="24">
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52 <!-- <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'/> -->
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53 <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'/>
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54 <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'/>
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55 <!-- <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'/> -->
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56 <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'/>
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57 <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'/>
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58 <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'/>
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59 <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'/>
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60 <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'/>
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61 <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'/>
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62 <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'/>
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63 <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'/>
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64 <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'/>
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65 <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'/>
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66 <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'/>
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67 <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'/>
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68 <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'/>
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69 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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parents: 0
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70 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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parents: 0
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71 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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72 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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parents: 0
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73 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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parents: 0
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74 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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75 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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76 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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77 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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78 </output_collection>
0
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79
1
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80 <output_collection name="outputFastqsReverse" type="list" count="24">
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81 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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82 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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83 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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84 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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85 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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86 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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87 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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88 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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89 <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'/>
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90 <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'/>
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91 <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'/>
649c86cedcb4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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92 <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'/>
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93 <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'/>
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94 <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'/>
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95 <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'/>
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96 <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'/>
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97 <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'/>
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98 <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'/>
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99 <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'/>
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100 <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'/>
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101 <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'/>
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102 <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'/>
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103 <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'/>
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104 <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'/>
0
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105 </output_collection>
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106 </test>
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107 </tests>
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108 <help><![CDATA[
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109
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110 Demultiplexing of raw fastq files
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111 =================================
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112
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113 scHicDemultiplex demultiplexes fastq files from Nagano 2017: "Cell-cycle dynamics of chromosomal organization at single-cell resolution" according their barcodes to
1
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114 a seperated forward and reverse strand fastq files per cell. For other datasets, a third-party demultiplexing strategy must be used.
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115
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116 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.
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117
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118 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
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119
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120 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
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121 ]]></help>
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122 <expand macro="citations" />
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123
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124 </tool>