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annotate 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
parents
children 4635a93ebd91
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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">
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2 <description>Generates an unmapped BAM file from fastq files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <version_command>fgbio --version</version_command>
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8 <command detect_errors="exit_code"><![CDATA[
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9 fgbio FastqToBam
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10 --input
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11 #for $input in $inputs
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12 '$input'
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13 #end for
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14 --sample='$sample'
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15 --library='$library'
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16 #if $read_structures:
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17 --read-structures $read_structures
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18 #end if
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19 --sort='$sort'
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20 --output '$output'
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21 ## optional bam header content
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22 #if $bam_header.umi_tag
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23 --umi-tag='$bam_header.umi_tag'
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24 #end if
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25 #if $bam_header.predicted_insert_size
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26 --predicted-insert-size='$bam_header.predicted_insert_size'
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27 #end if
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28 #if $bam_header.read_group
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29 --read-group='$bam_header.read_group'
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30 #end if
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31 #if $bam_header.description
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32 --description='$bam_header.description'
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33 #end if
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34 #if $bam_header.platform
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35 --platform='$bam_header.platform'
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36 #end if
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37 #if $bam_header.platform_model
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38 --platform-model='$bam_header.platform_model'
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39 #end if
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40 #if $bam_header.platform_model
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41 --platform-model='$bam_header.platform_model'
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42 #end if
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43 #if $bam_header.platform_unit
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44 --platform-unit='$bam_header.platform_unit'
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45 #end if
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46 #if $bam_header.sequencing_center
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47 --sequencing-center='$bam_header.sequencing_center'
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48 #end if
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49 #if $bam_header.comment
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50 --comment='$bam_header.comment'
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51 #end if
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52 ]]></command>
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53 <inputs>
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54 <param name="inputs" type="data" format="fastq" multiple="true" label="Fastq files corresponding to each sequencing read"/>
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55 <param argument="--sample" type="text" value="" label="The name of the sequenced sample">
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56 </param>
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57 <param argument="--library" type="text" value="" label="The name/ID of the sequenced library">
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58 </param>
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59 <param argument="--read-structures" type="text" value="" optional="true" label="Read structures, one for each of the FASTQ">
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60 <expand macro="read_structures_validator" />
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61 </param>
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62 <param argument="--sort" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Sort bam by queryname"
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63 help="If true, queryname sort the BAM file, otherwise preserve input order."/>
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64 <section name="bam_header" title="BAM Header" expanded="false">
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65 <param argument="--umi-tag" type="text" value="" optional="true" label="Tag in which to store molecular barcodes/UMIs" help="Default: RX">
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66 <expand macro="sam_tag_validator" />
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67 </param>
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68 <param argument="--predicted-insert-size" type="integer" value="" optional="true" label="Predicted median insert size, to insert into the read group header"/>
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69 <param argument="--read-group" type="text" value="" optional="true" label="Read group ID to use in the file header" help="Default: A"/>
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70 <param argument="--description" type="text" value="" optional="true" label="Description of the read group"/>
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71 <param argument="--platform" type="text" value="" optional="true" label="Sequencing Platform" help="Default: illumina"/>
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72 <param argument="--platform-model" type="text" value="" optional="true" label="Platform model to insert into the group header (ex. miseq, hiseq2500, hiseqX)"/>
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73 <param argument="--platform-unit" type="text" value="" optional="true" label="Platform unit (e.g. 'flowcell-barcode.lane.sample-barcode')"/>
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74 <param argument="--sequencing-center" type="text" value="" optional="true" label="The sequencing center from which the data originated"/>
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75 <param argument="--comment" type="text" value="" optional="true" label="Comment to include in the output header"/>
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76 </section>
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77 </inputs>
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78 <outputs>
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79 <data name="output" format="unsorted.bam" />
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80 </outputs>
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81 <help><![CDATA[
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82 **fgbio FastqToBam**
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83
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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.
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85
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86 @READ_STRUCTURES_HELP@
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87
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88 http://fulcrumgenomics.github.io/fgbio/tools/latest/FastqToBam.html
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89 ]]></help>
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90 <expand macro="citations" />
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91 </tool>