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comparison sinto_barcode.xml @ 0:3456ec59ff7a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
author iuc
date Thu, 13 Apr 2023 11:03:17 +0000
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1 <tool id="sinto_barcode" name="Sinto barcode" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>add cell barcodes to FASTQ read names</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">sinto</requirement>
8 </requirements>
9 <version_command>sinto --version</version_command>
10 <command><![CDATA[
11 ln -s '$barcode_fastq' barcodes.fastq.gz &&
12 ln -s '${fastq_input.read1_fastq}' read1.fastq.gz &&
13 #if str( $fastq_input.fastq_input_selector ) == "paired":
14 ln -s '${fastq_input.read2_fastq}' read2.fastq.gz &&
15 #end if
16 sinto barcode
17 --barcode_fastq barcodes.fastq.gz
18 --read1 read1.fastq.gz
19 #if str( $fastq_input.fastq_input_selector ) == "paired":
20 --read2 read2.fastq.gz
21 #end if
22 --bases $bases
23 ]]> </command>
24 <inputs>
25 <param type="data" name="barcode_fastq" format="fastqsanger.gz" label="FASTQ file containing cell barcode sequences" />
26 <conditional name="fastq_input">
27 <param name="fastq_input_selector" type="select" label="Single or Paired-end data">
28 <option value="paired">Paired</option>
29 <option value="single">Single</option>
30 </param>
31 <when value="paired">
32 <param name="read1_fastq" type="data" format="fastqsanger.gz" label="Forward reads FASTQ file" />
33 <param name="read2_fastq" type="data" format="fastqsanger.gz" label="Reverse reads FASTQ file" />
34 </when>
35 <when value="single">
36 <param name="read1_fastq" type="data" format="fastqsanger.gz" label="Select FASTQ file" />
37 </when>
38 </conditional>
39 <param type="integer" name="bases" value="16" min="0" label="Number of bases to extract from barcode-containing FASTQ" />
40 </inputs>
41 <outputs>
42 <data name='read1_out' format='fastqsanger.gz' label="${tool.name} on ${on_string}: barcoded read 1" from_work_dir="read1.barcoded.fastq" />
43 <data name='read2_out' format='fastqsanger.gz' label="${tool.name} on ${on_string}: barcoded read 2" from_work_dir="read2.barcoded.fastq" >
44 <filter>fastq_input['fastq_input_selector'] == 'paired'</filter>
45 </data>
46 </outputs>
47 <tests>
48 <test expect_num_outputs="1">
49 <param name="barcode_fastq" value="barcodes.fastq.gz" />
50 <param name="fastq_input_selector" value="single"/>
51 <param name="read1_fastq" value="read1.fastq.gz" />
52 <output name="read1_out" file="read1.barcoded.fastq.gz" ftype="fastqsanger.gz" decompress="true" />
53 </test>
54 <test expect_num_outputs="2">
55 <param name="barcode_fastq" value="barcodes.fastq.gz" />
56 <param name="fastq_input_selector" value="paired"/>
57 <param name="read1_fastq" value="read1.fastq.gz" />
58 <param name="read2_fastq" value="read2.fastq.gz" />
59 <output name="read1_out" file="read1.barcoded.fastq.gz" ftype="fastqsanger.gz" decompress="true"/>
60 <output name="read2_out" file="read2.barcoded.fastq.gz" ftype="fastqsanger.gz" decompress="true"/>
61 </test>
62 </tests>
63 <help><![CDATA[
64
65 Sinto is a toolkit for processing aligned single-cell data.
66 --------------------------------------------------------------------------------------------------------------
67 Cell barcodes from one FASTQ file added to the read names of another, or the same, FASTQ file. This is useful when processing raw single-cell sequencing data, as the cell barcode information can easily be propagated to the aligned BAM file by encoding the cell barcode in the read name.
68
69 **Inputs**
70 FASTQ files containing barcodes and forward reads. An optional reverse reads FASTQ file can be provided for paired-end experiments. Note that all the FASTQs must contain the same number of reads and the reads must appear in the same order.
71
72 **Outputs**
73 FASTQ files with the read names modified to contain the cell barcode sequence at the beginning of the read name, separated from the original read name by a : character.
74
75 ]]> </help>
76 <expand macro="citations" />
77 </tool>