Mercurial > repos > jjohnson > fgbio_fastq_to_bam

comparison fgbio_fastq_to_bam.xml @ 2:6137ff37bea1 draft default tip

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"planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
author jjohnson
date Thu, 19 Aug 2021 15:11:08 +0000
parents 4635a93ebd91
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1:4635a93ebd91 2:6137ff37bea1
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <version_command>fgbio --version</version_command> 7 <version_command>fgbio --version</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 @LINK_FASTQ_INPUTS@
9 fgbio FastqToBam 10 fgbio FastqToBam
10 --input 11 @FASTQ_INPUTS@
11 #for $input in $inputs
12 '$input'
13 #end for
14 --sample='$sample' 12 --sample='$sample'
15 --library='$library' 13 --library='$library'
16 #if $read_structures:
17 --read-structures $read_structures
18 #end if
19 --sort='$sort' 14 --sort='$sort'
20 --output '$output' 15 --output '$output'
21 ## optional bam header content 16 ## optional bam header content
22 #if $bam_header.umi_tag 17 #if $bam_header.umi_tag
23 --umi-tag='$bam_header.umi_tag' 18 --umi-tag='$bam_header.umi_tag'
49 #if $bam_header.comment 44 #if $bam_header.comment
50 --comment='$bam_header.comment' 45 --comment='$bam_header.comment'
51 #end if 46 #end if
52 ]]></command> 47 ]]></command>
53 <inputs> 48 <inputs>
54 <param name="inputs" type="data" format="fastq" multiple="true" label="Fastq files corresponding to each sequencing read"/> 49 <expand macro="fastq_inputs"/>
55 <param argument="--sample" type="text" value="" label="The name of the sequenced sample"> 50 <param argument="--sample" type="text" value="" label="The name of the sequenced sample">
51 <validator type="empty_field"/>
56 </param> 52 </param>
57 <param argument="--library" type="text" value="" label="The name/ID of the sequenced library"> 53 <param argument="--library" type="text" value="" label="The name/ID of the sequenced library">
58 </param> 54 <validator type="empty_field"/>
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> 55 </param>
62 <param argument="--sort" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sort bam by queryname" 56 <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."/> 57 help="If true, queryname sort the BAM file, otherwise preserve input order."/>
64 <section name="bam_header" title="BAM Header" expanded="false"> 58 <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"> 59 <param argument="--umi-tag" type="text" value="" optional="true" label="Tag in which to store molecular barcodes/UMIs" help="Default: RX">