Mercurial > repos > jjohnson > fgbio_fastq_to_bam
comparison fgbio_fastq_to_bam.xml @ 2:6137ff37bea1 draft default tip
"planemo upload commit 77a5370a0978b5332bb3a9f063588a52a468ea08"
| author | jjohnson |
|---|---|
| date | Thu, 19 Aug 2021 15:11:08 +0000 |
| parents | 4635a93ebd91 |
| children |
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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"> |