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"planemo upload for repository https://github.com/hCoV-2019/pangolin commit 9e569ed56e07b5d2d3fb8a72ddc477d34570f081"
author nml
date Fri, 29 May 2020 00:37:50 -0400
parents 35566aadcfc7
children
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1 <tool id="pangolin" name="Pangolin" version="@VERSION@+galaxy0">
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2 <description> CoV-2019 Phylogenetic Assignment of Named Global Outbreak LINeages</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 <command detect_errors="exit_code"><![CDATA[
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8
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9 pangolin '$input1' -t "\${GALAXY_SLOTS:-1}" --max-ambig '$additional.max_ambig' --min-length '$additional.min_length' $additional.write_tree $additional.include_putative &&
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10
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11 sed 's/,/\t/g' lineage_report.csv > lineage_report.tsv
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12 ]]></command>
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13 <inputs>
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14 <param name="input1" type="data" format="fasta"
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15 label="Input multi-sequence fasta file"
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16 />
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17 <section name="additional" title="Additional Parameters" expanded="false">
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18 <param name="max_ambig" type="float" value="0.5" min="0" max="1.0"
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19 label="Maximum proportion of Ns allowed to attempt assignment"
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20 argument="--max-ambig"
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21 />
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22 <param name="min_length" type="integer" value="10000" min="0"
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23 label="Minimum query length to attempt assignment"
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24 argument="--min-length"
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25 />
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26 <param name="include_putative" type="boolean" checked="false" argument="-p"
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27 truevalue="-p"
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28 falsevalue=""
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29 label="Include putative lineages"
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30 help="Putative lineages fit the criteria required for lineage designation but have not got recall values suitable for lineage assignment.
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31 If left as 'No', only lineages with >95% recall rate will be used."
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32 />
2
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33 <param name="write_tree" type="boolean" checked="false"
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34 truevalue="--write-tree"
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35 falsevalue=""
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36 label="Write guide trees"
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37 help="Output a collection of trees with each query sequence placed in the guide tree"
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38 />
0
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39 </section>
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40 </inputs>
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41 <outputs>
1
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42 <data format="tabular" from_work_dir="lineage_report.tsv" name="lineage_report" label="${input1.name}_lineage_report" />
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43 <collection name="pangolin_trees" type="list" label="${tool.name} Trees">
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44 <filter>additional['write_tree']</filter>
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45 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.tree" directory="pangolin_trees/" format="iqtree" />
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46 </collection>
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="input1" value="test_seqs.fasta" />
3
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51 <output name="lineage_report" >
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52 <assert_contents>
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53 <has_text text="Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17" />
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54 <has_text text="USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16" />
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55 <has_text text="This_seq_is_too_short" />
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56 <has_text text="lineage" />
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57 </assert_contents>
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58 </output>
0
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59 </test>
2
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60 <test>
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61 <param name="input1" value="test_seqs.fasta" />
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62 <section name="additional">
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63 <param name="write_tree" value="true" />
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64 <param name="include_putative" value="true" />
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65 </section>
3
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66 <output name="lineage_report" >
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67 <assert_contents>
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68 <has_text text="Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17" />
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69 <has_text text="USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16" />
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70 <has_text text="This_seq_is_too_short" />
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71 <has_text text="lineage" />
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72 </assert_contents>
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73 </output>
2
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74 <output_collection name="pangolin_trees" type="list">
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75 <element name="USA_NY-NYUMC7_2020_EPI_ISL_418192__USA_New_York_Manhattan_2020-03-16" ftype="iqtree">
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76 <assert_contents>
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77 <has_text text="USA/NY-NYUMC7/2020|EPI_ISL_418192||USA|New_York|Manhattan|2020-03-16" />
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78 </assert_contents>
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79 </element>
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80 <element name="Japan_DP0779_2020_EPI_ISL_416626__Japan_unknown__2020-02-17" ftype="iqtree">
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81 <assert_contents>
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82 <has_text text="Japan/DP0779/2020|EPI_ISL_416626||Japan|unknown||2020-02-17" />
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83 </assert_contents>
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84 </element>
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85 </output_collection>
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86 </test>
0
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87 </tests>
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88 <help><![CDATA[
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89
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90 Pangolin
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91 --------
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92
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93 Pangolin assigns SARS-CoV-2 genome sequences in fasta format to global lineages from `Rambaut et al. <https://doi.org/10.1101/2020.04.17.046086>`_.
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94 To do this, Pangolin employs the use of external programs including: `iqtree <http://www.iqtree.org/#download>`_, `mafft <https://mafft.cbrc.jp/alignment/software/>`_,
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95 and `snakemake <https://snakemake.readthedocs.io/en/stable/index.html>`_.
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96
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97 More information can be obtained from the authors github site: https://github.com/hCoV-2019/pangolin
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98
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99 You may also wish to visit the authors website at https://pangolin.cog-uk.io/
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100
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101 --------------
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102
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103 **Input** - Multi sequence fasta file or individual fasta files
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104
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105
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106 **Output** - lineage report:
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107
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108 +---------+---------+------+-------------+------------------+-----------+-----------+
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109 | Taxon | Lineage | aLRT | UFbootstrap | lineages_version | status | note |
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110 +=========+=========+======+=============+==================+===========+===========+
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111 | Sample1 | A.1 | 100 | 60 | 2020-04-27 | passed_qc | |
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112 +---------+---------+------+-------------+------------------+-----------+-----------+
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113 | Sample2 | B.1 | 80 | 80 | 2020-04-27 | passed_qc | |
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114 +---------+---------+------+-------------+------------------+-----------+-----------+
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115 | Sample3 | B.1.4 | 60 | 100 | 2020-04-27 | fail | seq_len:0 |
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116 +---------+---------+------+-------------+------------------+-----------+-----------+
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117
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118
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119 Resources for interpreting aLRT and UFbootstrap values:
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120
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121 - `IQ_TREE: Assessing branch supports with single branch tests <http://www.iqtree.org/doc/Tutorial#assessing-branch-supports-with-single-branch-tests>`_
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122
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123 - `IQ_TREE: Command Reference <http://www.iqtree.org/doc/Command-Reference>`_
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124
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125 ]]></help>
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126 <expand macro="citations" />
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127 </tool>