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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/tatajuba commit 6639e2954efcd909b3edcc139f8c9a48035bec0d-dirty
author thanhlv
date Wed, 15 Jun 2022 09:23:50 +0000
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1 <tool id="tatajuba" name="tatajuba" version="@VERSION@">
1
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2 <description> Finding distribution of homopolymeric tracts</description>
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3 <macros>
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4 <token name="@VERSION@">1.0.4</token>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">tatajuba</requirement>
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8 </requirements>
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9 <version_command>tatajuba --version</version_command>
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10 <command detect_errors="exit_code"><![CDATA[
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11 #if $reads.sr_type == "paired"
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12 ln -s '$reads.R1' read1.fastq.gz &&
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13 ln -s '$reads.R2' read2.fastq.gz &&
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14 #end if
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15 #if $reads.sr_type == "collection"
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16 ln -s '$reads.input1.forward' read1.fastq.gz &&
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17 ln -s '$reads.input1.reverse' read2.fastq.gz &&
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18 #end if
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19 ln -s '$gff' 'ref.gff' &&
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20 ln -s '$fasta' 'ref.fasta' &&
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21 tatajuba
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22 $keep_bias
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23 $vcf
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24 --kmer=$kmer
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25 --minsize=$minsize
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26 --minreads=$minreads
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27 --maxdist=$maxdist
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28 #if $leven > 0
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29 --level $leven
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30 #end if
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31 --nthreads=\${GALAXY_SLOTS:-4}
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32 --gff=ref.gff
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33 --fasta=ref.fasta
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34 *.fastq.gz
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35 --outdir=output
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36 ]]> </command>
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37
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38 <inputs>
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39 <conditional name="reads">
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40 <param name="sr_type" type="select" label="Input reads type or collection" help="Select 'paired end' for a single library or 'collection' for a paired end collection">
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41 <option value="paired" selected="true">Paired End</option>
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42 <option value="collection">Paired Collection</option>
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43 </param>
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44 <when value="paired">
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45 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
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46 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
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47 </when>
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48 <when value="collection">
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49 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>
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50 </when>
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51 </conditional>
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52 <param name="gff" type="data" format="gff" label="Reference in GFF format"/>
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53 <param name="fasta" type="data" format="fasta,fasta.gz" label="Reference in fasta format"/>
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54 <param argument="kmer" type="integer" value="25" min="2" max="32" label="Kmer size flanking each side of homopolymer" />
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55 <param argument="minsize" type="integer" value="4" min="1" max="32" label="Fraction value of the read depth to be considered invalid" />
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56 <param argument="minreads" type="integer" value="5" min="1" label="Minimum number of reads for tract+context to be considered" />
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57 <param argument="maxdist" type="integer" value="1" min="1" label="Maximum distance between kmers of a flanking region to merge them into one context" />
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58 <param argument="leven" type="integer" value="0" min="0" label="Levenshtein distance between flanking regions to merge them into one context" />
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59 <param argument="vcf" type="boolean" truevalue="--vcf" falsevalue="" checked="false" label="generate VCF files for each sample, around the HT regions" />
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60 <param argument="keep_bias" type="boolean" truevalue="--keep_bias" falsevalue="" checked="false" label="Keep biased tracts" />
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61 </inputs>
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62 <outputs>
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63 <data name="variable_tracts" format="tabular" from_work_dir="output/variable_tracts.bed" label="${tool.name} on ${on_string} BED file with tract locations" />
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64 <data name="tract_list" format="tabular" from_work_dir="output/tract_list.tsv" label="${tool.name} on ${on_string} list of all HTs found" />
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65 <data name="selected_tracts_unknown" format="tabular" from_work_dir="output/selected_tracts_unknown.tsv" label="${tool.name} on ${on_string} debug file with difference stats per tract for tracts outside annotated regions" />
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66 <data name="selected_tracts_annotated" format="tabular" from_work_dir="output/selected_tracts_annotated.tsv" label="${tool.name} on ${on_string} debug file with difference stats per tract for tracts in annotated regions" />
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67 <data name="per_sample_proportional_coverage" format="tabular" from_work_dir="output/per_sample_proportional_coverage.tsv" label="${tool.name} on ${on_string} feature matrix of proportional coverage depth of HT" />
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68 <data name="per_sample_proportional_coverage" format="tabular" from_work_dir="output/per_sample_modal_frequency.tsv" label="${tool.name} on ${on_string} feature matrix with histogram bar length of modal tract length" />
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69 <data name="per_sample_average_length" format="tabular" from_work_dir="output/per_sample_average_length.tsv" label="${tool.name} on ${on_string} feature matrix with average HT length" />
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70 <data name="vcf1" format="vcf" from_work_dir="output/1.vcf.gz" label="${tool.name} on ${on_string} VCF-1" />
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71 <data name="vcf2" format="vcf" from_work_dir="output/2.vcf.gz" label="${tool.name} on ${on_string} VCF-2" />
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72 </outputs>
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73 <tests>
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74 <test name="test-paired-end">
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75 <param name="sr_type" value="paired" />
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76 <param name="R1" value="r1.fastq.gz" ftype="fastqsanger.gz" />
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77 <param name="R2" value="r2.fastq.gz" ftype="fastqsanger.gz" />
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78 <param name="gff" value="GCF_000009085.1_ASM908v1_genomic.gff" ftype="gff" />
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79 <param name="fasta" value="GCF_000009085.1_ASM908v1_genomic.fna" ftype="fasta" />
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80 <output name="per_sample_average_length" file="output/per_sample_average_length.tsv" ftype="tabular" compare="contains" />
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81 </test>
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82 </tests>
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83 <help><![CDATA[
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84 ]]> </help>
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85 </tool>