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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu commit 4290547cefb0459595f28fbba063f2cf58b35086
author iuc
date Tue, 13 Aug 2024 13:44:35 +0000
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d4cc7bbf4a14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pacu commit 4290547cefb0459595f28fbba063f2cf58b35086
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1 <tool id="pacu_map" name="PACU - mapping" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Map ONT / Illumina reads to a reference genome for PACU</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='xrefs'/>
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7 <expand macro="requirements" />
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 PACU_map
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12
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13 ## FASTA input
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14 --ref-fasta '$ref_fasta'
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15 --ref-fasta-name '$ref_fasta.element_identifier'
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16
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17 ## FASTQ input
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18 --read-type $fastq_tech.read_type
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19 #if str($fastq_tech.read_type) == 'illumina':
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20 --fastq-illumina $fastq_tech.fastq_illumina_1 $fastq_tech.fastq_illumina_2
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21 --fastq-illumina-names '$fastq_tech.fastq_illumina_1.element_identifier' '$fastq_tech.fastq_illumina_2.element_identifier'
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22 #elif str($fastq_tech.read_type) == 'ont':
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23 --fastq-ont $fastq_tech.fastq_ont
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24 --fastq-ont-name '$fastq_tech.fastq_ont.element_identifier'
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25 #end if
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26
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27 ## Output
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28 --output '$bam'
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29
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30 ## Other options
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31 $trim
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32 --dir-working \$PWD
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33 --threads \${GALAXY_SLOTS}
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34 ]]>
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35 </command>
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36 <inputs>
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37 <param argument="--ref-fasta" type="data" format="fasta" label="Reference genome"/>
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38 <conditional name="fastq_tech">
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39 <param argument="--read-type" type="select" label="FASTQ type">
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40 <option value="illumina">Illumina paired-end reads</option>
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41 <option value="ont">ONT single-end reads</option>
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42 </param>
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43 <when value="illumina">
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44 <param name="fastq_illumina_1" type="data" format="fastq,fastqsanger.gz" label="Forward reads"/>
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45 <param name="fastq_illumina_2" type="data" format="fastq,fastqsanger.gz" label="Reverse reads"/>
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46 </when>
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47 <when value="ont">
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48 <param name="fastq_ont" type="data" format="fastq,fastqsanger.gz" label="ONT reads"/>
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49 </when>
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50 </conditional>
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51 <param argument="--trim" type="boolean" label="Trim reads" checked="true" truevalue="--trim" falsevalue=""/>
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52 </inputs>
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53 <outputs>
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54 <data name="bam" format="bam" label="Mapping on ${on_string}"/>
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55 </outputs>
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56 <tests>
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57 <test>
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58 <!-- The line differences correspond to the three commands in the SAM header -->
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59 <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
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60 <conditional name="fastq_tech">
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61 <param name="read_type" value="ont"/>
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62 <param name="fastq_ont" value="TIAC1151-ont.gz"/>
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63 </conditional>
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64 <param name="trim" value="false" />
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65 <output name="bam" ftype="bam" file="mapped_reads-ont.bam" lines_diff="6"/>
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66 </test>
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67 <test>
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68 <!-- The line differences correspond to the three commands in the SAM header -->
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69 <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
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70 <conditional name="fastq_tech">
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71 <param name="read_type" value="illumina"/>
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72 <param name="fastq_illumina_1" value="TIAC1151_1P.fastq.gz"/>
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73 <param name="fastq_illumina_2" value="TIAC1151_2P.fastq.gz"/>
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74 </conditional>
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75 <param name="trim" value="false" />
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76 <output name="bam" ftype="bam" file="mapped_reads-ilmn.bam" lines_diff="6"/>
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77 </test>
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78 <test>
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79 <!-- The line differences correspond to the three commands in the SAM header -->
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80 <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
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81 <conditional name="fastq_tech">
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82 <param name="read_type" value="ont"/>
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83 <param name="fastq_ont" value="TIAC1151-ont.gz"/>
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84 </conditional>
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85 <param name="trim" value="true" />
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86 <output name="bam" ftype="bam" file="mapped_reads_trimmed-ont.bam" lines_diff="6"/>
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87 </test>
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88 <test>
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89 <!-- The line differences correspond to the three commands in the SAM header -->
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90 <param name="ref_fasta" value="NC_002695.2-subset.fasta"/>
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91 <conditional name="fastq_tech">
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92 <param name="read_type" value="illumina"/>
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93 <param name="fastq_illumina_1" value="TIAC1151_1P.fastq.gz"/>
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94 <param name="fastq_illumina_2" value="TIAC1151_2P.fastq.gz"/>
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95 </conditional>
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96 <param name="trim" value="true" />
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97 <output name="bam" ftype="bam" file="mapped_reads_trimmed-ilmn.bam" lines_diff="6"/>
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98 </test>
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99 </tests>
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100 <help>
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101 This script maps Illumina or ONT reads to an input reference genome in FASTA format.
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102 It also writes a custom tag to the BAM file to propagate the sample name to PACU within Galaxy.
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103 The sample name is derived from the name of the input FASTQ files.
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104 </help>
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105 <expand macro="citations"/>
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106 </tool>