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comparison fgbio_fastq_to_bam.xml @ 0:ee774248788f draft

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"planemo upload commit 61f6c8e7f32f170ad7e66e46dd74e8c5d361a722"
author jjohnson
date Sun, 21 Feb 2021 23:40:09 +0000
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1 <tool id="fgbio_fastq_to_bam" name="fgbio FastqToBam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
2 <description>Generates an unmapped BAM file from fastq files</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <version_command>fgbio --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[
9 fgbio FastqToBam
10 --input
11 #for $input in $inputs
12 '$input'
13 #end for
14 --sample='$sample'
15 --library='$library'
16 #if $read_structures:
17 --read-structures $read_structures
18 #end if
19 --sort='$sort'
20 --output '$output'
21 ## optional bam header content
22 #if $bam_header.umi_tag
23 --umi-tag='$bam_header.umi_tag'
24 #end if
25 #if $bam_header.predicted_insert_size
26 --predicted-insert-size='$bam_header.predicted_insert_size'
27 #end if
28 #if $bam_header.read_group
29 --read-group='$bam_header.read_group'
30 #end if
31 #if $bam_header.description
32 --description='$bam_header.description'
33 #end if
34 #if $bam_header.platform
35 --platform='$bam_header.platform'
36 #end if
37 #if $bam_header.platform_model
38 --platform-model='$bam_header.platform_model'
39 #end if
40 #if $bam_header.platform_model
41 --platform-model='$bam_header.platform_model'
42 #end if
43 #if $bam_header.platform_unit
44 --platform-unit='$bam_header.platform_unit'
45 #end if
46 #if $bam_header.sequencing_center
47 --sequencing-center='$bam_header.sequencing_center'
48 #end if
49 #if $bam_header.comment
50 --comment='$bam_header.comment'
51 #end if
52 ]]></command>
53 <inputs>
54 <param name="inputs" type="data" format="fastq" multiple="true" label="Fastq files corresponding to each sequencing read"/>
55 <param argument="--sample" type="text" value="" label="The name of the sequenced sample">
56 </param>
57 <param argument="--library" type="text" value="" label="The name/ID of the sequenced library">
58 </param>
59 <param argument="--read-structures" type="text" value="" optional="true" label="Read structures, one for each of the FASTQ">
60 <expand macro="read_structures_validator" />
61 </param>
62 <param argument="--sort" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sort bam by queryname"
63 help="If true, queryname sort the BAM file, otherwise preserve input order."/>
64 <section name="bam_header" title="BAM Header" expanded="false">
65 <param argument="--umi-tag" type="text" value="" optional="true" label="Tag in which to store molecular barcodes/UMIs" help="Default: RX">
66 <expand macro="sam_tag_validator" />
67 </param>
68 <param argument="--predicted-insert-size" type="integer" value="" optional="true" label="Predicted median insert size, to insert into the read group header"/>
69 <param argument="--read-group" type="text" value="" optional="true" label="Read group ID to use in the file header" help="Default: A"/>
70 <param argument="--description" type="text" value="" optional="true" label="Description of the read group"/>
71 <param argument="--platform" type="text" value="" optional="true" label="Sequencing Platform" help="Default: illumina"/>
72 <param argument="--platform-model" type="text" value="" optional="true" label="Platform model to insert into the group header (ex. miseq, hiseq2500, hiseqX)"/>
73 <param argument="--platform-unit" type="text" value="" optional="true" label="Platform unit (e.g. 'flowcell-barcode.lane.sample-barcode')"/>
74 <param argument="--sequencing-center" type="text" value="" optional="true" label="The sequencing center from which the data originated"/>
75 <param argument="--comment" type="text" value="" optional="true" label="Comment to include in the output header"/>
76 </section>
77 </inputs>
78 <outputs>
79 <data name="output" format="unsorted.bam" />
80 </outputs>
81 <help><![CDATA[
82 **fgbio FastqToBam**
83
84 Generates an unmapped BAM (or SAM or CRAM) file from fastq files. Takes in one or more fastq files (optionally gzipped), each representing a different sequencing read (e.g. R1, R2, I1 or I2) and can use a set of read structures to allocate bases in those reads to template reads, sample indices, unique molecular indices, or to designate bases to be skipped over.
85
86 @READ_STRUCTURES_HELP@
87
88 http://fulcrumgenomics.github.io/fgbio/tools/latest/FastqToBam.html
89 ]]></help>
90 <expand macro="citations" />
91 </tool>