Mercurial > repos > jjohnson > fgbio_fastq_to_bam

comparison fgbio_fastq_to_bam.xml @ 1:4635a93ebd91 draft

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"planemo upload commit 692ea558cbbefee93859dc2b005fab5ac4970eb8"
author jjohnson
date Wed, 24 Feb 2021 13:01:53 +0000
parents ee774248788f
children 6137ff37bea1
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0:ee774248788f 1:4635a93ebd91
74 <param argument="--sequencing-center" type="text" value="" optional="true" label="The sequencing center from which the data originated"/> 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"/> 75 <param argument="--comment" type="text" value="" optional="true" label="Comment to include in the output header"/>
76 </section> 76 </section>
77 </inputs> 77 </inputs>
78 <outputs> 78 <outputs>
79 <data name="output" format="unsorted.bam" /> 79 <data name="output" format="bam" >
80 <expand macro="sort_order_change_format" />
81 </data>
80 </outputs> 82 </outputs>
81 <help><![CDATA[ 83 <help><![CDATA[
82 **fgbio FastqToBam** 84 **fgbio FastqToBam**
83 85
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. 86 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.