Mercurial > repos > iuc > tbprofiler

annotate tb_profiler_profile.xml @ 0:8529c9fd63ad draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
author iuc
date Tue, 02 Apr 2019 09:03:16 -0400
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children 5182e1a99313
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8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
iuc
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1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="2.1.0">
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
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2 <description>Infer strain types and drug resistance markers from sequences</description>
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3 <requirements>
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4 <requirement type="package" version="2.1.0">tb-profiler</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 tb-profiler profile
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8
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9 --platform '${platform.value}'
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10
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11 #if $fastq_or_bam.input_select.value == "fastq":
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12 --read1 '${read1}'
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13
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
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14 #if $read2:
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15 --read2 '${read2}'
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16 #end if
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17
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18 #else if $fastq_or_bam.input_select.value == "bam":
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19 --bam '${bam_input}'
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20 #end if
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21
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22 --call_method '${call_method}'
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23 --min_depth '${min_depth}'
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24 --threads "\${GALAXY_SLOTS:-1}"
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25 --mapper '${mapper}'
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26 --min_gene_frac '${min_gene_frac}'
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27
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28 #if $txt:
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29 --txt
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30 #end if
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31
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32 ]]></command>
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33 <inputs>
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34 <param name="platform" type="select" label="Platform">
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35 <option value="Illumina" selected="true">Illumina</option>
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36 <option value="minION">minION</option>
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37 </param>
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38 <conditional name="fastq_or_bam">
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39 <param name="input_select" type="select" label="Input File Type">
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40 <option value="fastq">fastq</option>
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41 <option value="bam">bam</option>
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42 </param>
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43 <when value="fastq">
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44 <param name="read1" type="data" format="fastq" label="Read1" help="First read file (default: None)"/>
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45 <param name="read2" type="data" format="fastq" optional="true" label="Read2" help="Second read file (default: None)"/>
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46 </when>
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47 <when value="bam">
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48 <param name="bam_input" type="data" format="bam" label="Bam" help="Warning!!!: The BAM files must have been created using the ensembl version of the genome."/>
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49 </when>
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50 </conditional>
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51 <param name="call_method" type="select" label="Call Method" help="Level of quality stringency required. (default: low)">
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52 <option value="low" selected="true">low</option>
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53 <option value="high">high</option>
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54 <option value="optimise">optimise</option>
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55 </param>
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56 <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/>
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57 <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
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58 <option value="bwa" selected="true">bwa</option>
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59 <option value="minimap2">minimap2</option>
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60 <option value="bowtie2">bowtie2</option>
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61 </param>
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62 <param name="min_gene_frac" label="Minimum Gene Fraction" type="float" value="0.9" help="Used to infer a deletion if the fraction of a gene covered falls below this value. Also used to see if sample is high quality to continue by checking the fraction for rpoB (where deletion should not occur). (default: 0.9)"/>
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63 <param name="txt" label="Generate text file ouput" type="boolean" value="false" help="Create reader-friendly text output in addition to standard JSON output (default: False)"/>
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64 </inputs>
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65 <outputs>
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66 <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/>
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67 <data name="results_txt" format="txt" from_work_dir="results/tbprofiler.results.txt" label="${tool.name} on ${on_string}: Results.txt">
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68 <filter>txt</filter>
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69 </data>
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70 </outputs>
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71 <tests>
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72 <test expect_num_outputs="1">
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73 <param name="read1" value="rif_resistant.fastq.gz"/>
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74 <output name="results_json" value="results_1.json"/>
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75 </test>
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76 <test expect_num_outputs="2">
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77 <param name="read1" value="rif_resistant.fastq.gz"/>
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78 <param name="txt" value="true"/>
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79 <param name="call_method" value="high"/>
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80 <param name="min_depth" value="11"/>
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81 <output name="results_json" value="results_2.json"/>
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82 <output name="results_txt" value="results_2.txt"/>
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83 </test>
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84 </tests>
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85 <help><![CDATA[
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86 Summary
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87 =======
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88
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89 The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using SAMtools. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data).
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90
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91 Produces a JSON output file by default.
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92
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93 ]]></help>
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94 <citations>
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95 <citation type="bibtex">
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96 @UNPUBLISHED{Phelan2016,
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97 author = {Phelan, Jody},
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98 title = {TBProfiler},
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99 year = {2016},
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100 url = {https://github.com/jodyphelan/TBProfiler},
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101 }
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102 </citation>
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103 </citations>
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104 </tool>