Mercurial > repos > iuc > schicexplorer_schicdemultiplex

comparison scHicDemultiplex.xml @ 0:e59d83af97a1 draft

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"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
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children 649c86cedcb4
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-1:000000000000 0:e59d83af97a1
1 <tool id="schicexplorer_schicdemultiplex" name="@BINARY@" version="@WRAPPER_VERSION@.0">
2 <description>demultiplexes Nagano 2017 raw fastq files</description>
3 <macros>
4 <token name="@BINARY@">scHicDemultiplex</token>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <command detect_errors="exit_code"><![CDATA[
9 #import re
10 mkdir outputFiles &&
11 #set fastqFile = @ESCAPE_IDENTIFIER_FASTQ@
12 ln -s '$fastq' '$fastqFile' &&
13 @BINARY@
14
15 --fastq $fastqFile
16 --barcodeFile '$barcodeFile'
17 --srrToSampleFile '$srrToSample'
18 --outputFolder outputFiles
19 --bufferSize $bufferSize
20 --threads @THREADS@
21
22 ]]></command>
23 <inputs>
24
25 <param name='fastq' type="data" format="fastq, fastq.gz" label="Raw fastq file from Nagano 2017."/>
26 <param name='barcodeFile' type="data" format="txt" label="barcode file" help="Use GSE94489_README.txt file "/>
27 <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."/>
28 <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." />
29
30 </inputs>
31 <outputs>
32 <collection name="outputFastqs" type="list" label="Demultiplexed fastq files">
33 <discover_datasets pattern="__name__" format="fastq.gz" directory="outputFiles" />
34 </collection>
35 </outputs>
36 <tests>
37 <test>
38 <param name='fastq' value='scHicDemultiplex/SRR5229025.fastq.gz' ftype="fastq.gz" />
39 <param name='barcodeFile' value='scHicDemultiplex/GSE94489_README.txt' />
40 <param name='srrToSample' value='scHicDemultiplex/samples.txt' />
41 <param name='bufferSize' value='1000' />
42
43
44 <output_collection name="outputFastqs" type="list" count="48">
45 <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'/>
46 <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'/>
47 <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'/>
48 <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'/>
49 <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'/>
50 <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'/>
51 <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'/>
52 <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'/>
53 <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'/>
54 <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'/>
55 <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'/>
56 <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'/>
57 <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'/>
58 <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'/>
59 <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'/>
60 <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'/>
61 <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'/>
62 <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'/>
63 <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'/>
64 <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'/>
65 <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'/>
66 <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'/>
67 <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'/>
68 <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'/>
69 <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'/>
70 <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'/>
71 <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'/>
72 <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'/>
73 <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'/>
74 <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'/>
75 <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'/>
76 <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'/>
77 <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'/>
78 <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'/>
79 <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'/>
80 <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'/>
81 <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'/>
82 <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'/>
83 <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'/>
84 <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'/>
85 <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'/>
86 <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'/>
87 <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'/>
88 <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'/>
89 <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'/>
90 <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'/>
91 <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'/>
92 <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'/>
93 </output_collection>
94 </test>
95 </tests>
96 <help><![CDATA[
97
98 Demultiplexing of raw fastq files
99 =================================
100
101 scHicDemultiplex demultiplexes fastq files from Nagano 2017: "Cell-cycle dynamics of chromosomal organization at single-cell resolution" according their barcodes to
102 a seperated forward and reverse strand fastq files per cell.
103
104 For more information about scHiCExplorer please consider our documentation on readthedocs.io_
105
106 .. _readthedocs.io: http://schicexplorer.readthedocs.io/
107 ]]></help>
108 <expand macro="citations" />
109
110 </tool>