Mercurial > repos > ufz > phi_toolkit_report

annotate phitk.xml @ 1:3a7f73d638ba draft default tip

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planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
author ufz
date Tue, 22 Jul 2025 11:09:24 +0000
parents 315c2ed31af1
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315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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1 <tool id="phi_toolkit_report" name="PHI toolkit report" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01" license="MIT">
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2 <description></description>
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3 <icon src="logo.jpg"/>
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4 <macros>
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5 <token name="@TOOL_VERSION@">0.2.0</token>
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6 <token name="@VERSION_SUFFIX@">0</token>
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7
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8 <xml name="zenodo_collection_element" tokens="id" token_suffix="">
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9 <element name="@ID@@SUFFIX@" location="https://zenodo.org/records/15594463/files/@ID@.fasta.fasta?download=1" value="genomes/@ID@.fasta" ftype="fasta"/>
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10 </xml>
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12 <xml name="test_collection_element" tokens="id,folder,ext,suffix">
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13 <element name="@ID@@SUFFIX@" value="@FOLDER@/@ID@.fasta.@EXT@" ftype="@EXT@"/>
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14 </xml>
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15 <xml name="test_collection_non_empty" tokens="name,folder,ext" token_suffix="">
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16 <param name="@NAME@">
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17 <collection type="list">
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18 <expand macro="test_collection_element" id="NC_000913" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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19 <expand macro="test_collection_element" id="NC_002737" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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20 <expand macro="test_collection_element" id="NC_008261" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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21 <expand macro="test_collection_element" id="NC_009012" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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22 <expand macro="test_collection_element" id="NC_014168" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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23 <expand macro="test_collection_element" id="NC_014212" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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24 <expand macro="test_collection_element" id="NC_014364" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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25 <expand macro="test_collection_element" id="NC_015761" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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26 <expand macro="test_collection_element" id="NC_017033" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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27 <expand macro="test_collection_element" id="NC_018068" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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28 <expand macro="test_collection_element" id="NC_018515" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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29 <expand macro="test_collection_element" id="NC_019936" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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30 <expand macro="test_collection_element" id="NC_021184" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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31 <yield/>
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32 </collection>
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33 </param>
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34 </xml>
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35 <xml name="test_collection" tokens="name,folder,ext" token_suffix="">
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36 <expand macro="test_collection_non_empty" name="@NAME@" folder="@FOLDER@" ext="@EXT@" suffix="@SUFFIX@">
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37 <expand macro="test_collection_element" id="NC_003450" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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38 <expand macro="test_collection_element" id="NC_012982" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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39 <expand macro="test_collection_element" id="NC_014008" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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40 <expand macro="test_collection_element" id="NC_014211" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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41 <expand macro="test_collection_element" id="NC_014363" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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42 <expand macro="test_collection_element" id="NC_017095" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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43 <expand macro="test_collection_element" id="NC_018014" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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44 <expand macro="test_collection_element" id="NC_019897" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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45 <expand macro="test_collection_element" id="NC_019904" suffix="@SUFFIX@" folder="@FOLDER@" ext="@EXT@"/>
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46 </expand>
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47 </xml>
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48
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49 </macros>
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50 <!-- TODO <xrefs>
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51 <xref type="bio.tools"></xref>
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52 </xrefs> -->
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53 <requirements>
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54 <requirement type="package" version="2.74.0">bioconductor-biostrings</requirement>
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55 <requirement type="package" version="1.58.0">bioconductor-genomicranges</requirement>
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56 <requirement type="package" version="1.18.0">bioconductor-gmoviz</requirement>
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57 <requirement type="package" version="0.2.1">r-formattable</requirement>
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58 <requirement type="package" version="1.0.1">r-here</requirement>
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59 <requirement type="package" version="2.2.1">r-janitor</requirement>
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60 <requirement type="package" version="1.4.0">r-kableextra</requirement>
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61 <requirement type="package" version="1.3.0">r-patchwork</requirement>
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62 <requirement type="package" version="2.0.0">r-tidyverse</requirement>
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63 <requirement type="package" version="2.0.2">r-base64</requirement>
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64 <requirement type="package" version="3.5.0">r-pdftools</requirement>
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65 </requirements>
1
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66 <version_command><![CDATA[
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67 echo $(R --vanilla --slave -e 'required_packages <- c("tidyverse", "janitor", "here", "kableExtra", "gmoviz", "circlize", "GenomicRanges", "patchwork", "fs", "tools", "scales", "formattable", "pdftools", "base64"); invisible(lapply(required_packages, library, character.only = TRUE, quietly=TRUE, verbose=FALSE)); sessionInfo()' 2> /dev/null)
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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68 ]]></version_command>
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69 <command detect_errors="exit_code"><![CDATA[
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70 #import re
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71 mkdir -p data/genomes &&
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72 #for e in $genomes
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diff changeset
73 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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74 ln -s '$e' 'data/genomes/${id}.fna' &&
0
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
ufz
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diff changeset
75 #end for
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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diff changeset
76
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
ufz
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77 mkdir -p data/host_analyses &&
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
ufz
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78 mkdir -p data/virus_analyses &&
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
ufz
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diff changeset
79
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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diff changeset
80 ## checkm
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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81 mkdir -p data/host_analyses/checkm2 &&
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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diff changeset
82 ln -s '$checkm' data/host_analyses/checkm2/quality_report.tsv &&
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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diff changeset
83
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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diff changeset
84 ## defense-finder inputs
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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85 mkdir -p data/host_analyses/defense-finder &&
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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diff changeset
86 #for e in $defense_finder
1
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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parents: 0
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87 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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88 mkdir -p 'data/host_analyses/defense-finder/${id}/' &&
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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89 ln -s '$e' 'data/host_analyses/defense-finder/${id}/${id}_defense_finder_systems.tsv' &&
0
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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diff changeset
90 #end for
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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diff changeset
91
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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92 ## genomad inputs
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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93 mkdir -p data/host_analyses/genomad &&
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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diff changeset
94 #for e in $genomad
1
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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parents: 0
diff changeset
95 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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96 mkdir -p 'data/host_analyses/genomad/${id}/${id}_summary/' &&
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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97 ln -s '$e' 'data/host_analyses/genomad/${id}/${id}_summary/${id}_virus_summary.tsv' &&
0
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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98 #end for
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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99 #for e in $genomad_phages
1
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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100 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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101 mkdir -p 'data/host_analyses/genomad/${id}/${id}_summary/' &&
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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102 ln -s '$e' 'data/host_analyses/genomad/${id}/${id}_summary/${id}_virus.fna' &&
0
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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103 #end for
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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104 #for e in $genomad_annotations
1
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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105 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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106 mkdir -p 'data/host_analyses/genomad/${id}/${id}_summary/' &&
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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107 ln -s '$e' 'data/host_analyses/genomad/${id}/${id}_summary/${id}_virus_genes.tsv' &&
0
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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108 #end for
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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109
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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110 ## GTDBTK
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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111 mkdir -p data/host_analyses/gtdbtk &&
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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112 ln -s '$gtdb_summary' data/host_analyses/gtdbtk/gtdbtk.bac120.summary.tsv &&
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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113
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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114 ## CheckV
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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115 mkdir -p data/virus_analyses/checkv &&
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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116 #for e in $checkv
1
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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117 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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118 mkdir -p 'data/virus_analyses/checkv/${id}/' &&
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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119 ln -s '$e' 'data/virus_analyses/checkv/${id}/quality_summary.tsv' &&
0
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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120 #end for
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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121
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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122 ## drep compare
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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123 mkdir -p data/virus_analyses/drep_compare &&
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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124 #for e in $drep_compare
1
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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125 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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126 mkdir -p 'data/virus_analyses/drep_compare/${id}/data_tables' &&
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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127 ln -s '$e' 'data/virus_analyses/drep_compare/${id}/data_tables/Cdb.csv' &&
0
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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128 #end for
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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129 #for e in $drep_compare_clustering_dendrogram
1
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130 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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131 mkdir 'data/virus_analyses/drep_compare/${id}/figures/' &&
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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132 ln -s '$e' 'data/virus_analyses/drep_compare/${id}/figures/Primary_clustering_dendrogram.pdf' &&
0
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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133 #end for
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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134
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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135 ## iphop
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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136 mkdir -p data/virus_analyses/iphop &&
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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137 #for e in $iphop
1
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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138 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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139 mkdir -p 'data/virus_analyses/iphop/${id}/' &&
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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140 ln -s '$e' 'data/virus_analyses/iphop/${id}/Host_prediction_to_genome_m90.csv' &&
0
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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141 #end for
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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142
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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143 ## abricate
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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144 mkdir -p data/virus_analyses/abricate &&
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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145 #for e in $abricate
1
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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146 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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147 mkdir -p 'data/virus_analyses/abricate/${id}/' &&
3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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148 ln -s '$e' 'data/virus_analyses/abricate/${id}/${id}_virus_vfdb.tsv' &&
0
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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149 #end for
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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150
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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151 ## vibrant
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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152 mkdir -p data/virus_analyses/vibrant &&
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153 #for e in $vibrant
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154 #set id=re.sub(r'[^\w\-.]', '_', $e.element_identifier)
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155 mkdir -p 'data/virus_analyses/vibrant/${id}/VIBRANT_${id}_virus/VIBRANT_results_${id}_virus/' &&
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156 ln -s '$e' 'data/virus_analyses/vibrant/${id}/VIBRANT_${id}_virus/VIBRANT_results_${id}_virus/VIBRANT_AMG_individuals_${id}_virus.tsv' &&
0
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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157 #end for
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158
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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159 Rscript -e "library(rmarkdown); render('$__tool_directory__/report.Rmd', output_dir='"\$(pwd)"', output_format = 'html_document', intermediates_dir = '"\$(pwd)"', knit_root_dir='"\$(pwd)"')" &&
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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160 cp report.html '$report'
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161 && >&2 echo "debug.log:"
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162 && >&2 cat debug.log
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163 ]]></command>
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164 <inputs>
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165 <param type="data_collection" name="genomes" format="fasta" label="Genomes"/>
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166 <param type="data" name="checkm" format="tabular" label="Checkm2 quality report"/>
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167 <param type="data_collection" name="genomad" format="tabular" label="geNomad Virus Summary"/>
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168 <param type="data_collection" name="genomad_phages" format="fasta" label="geNomad Virus fasta"/>
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169 <param type="data_collection" name="genomad_annotations" format="tabular" label="geNomad Virus genes"/>
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170 <param type="data_collection" name="defense_finder" format="tabular" label="DefenseFinder systems"/>
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171 <param type="data" name="gtdb_summary" format="tsv" label="GTDB-Tk summary"/>
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172 <param type="data_collection" name="checkv" format="tabular" label="CheckV Quality summary"/>
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173 <param type="data_collection" name="drep_compare" format="csv" label="drep compare Cdb.csv"/>
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174 <param type="data_collection" name="drep_compare_clustering_dendrogram" format="pdf" label="drep compare clustering dendrogram"/>
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175 <param type="data_collection" name="iphop" format="csv" label="iPHop Host prediction to genome"/>
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176 <param type="data_collection" name="abricate" format="tabular" label="Abricate results"/>
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177 <param type="data_collection" name="vibrant" format="tabular" label="Vibrant Individual predicted virus AMGs" help="Vibrant output option 'Individual predicted virus AMGs by protein and its respective genome'"/>
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178 </inputs>
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179 <outputs>
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180 <data name="report" format="html"/>
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181 </outputs>
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182 <tests>
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183 <test>
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184 <param name="genomes">
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185 <collection type="list">
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186 <expand macro="zenodo_collection_element" id="NC_000913"/>
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187 <expand macro="zenodo_collection_element" id="NC_002737"/>
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188 <expand macro="zenodo_collection_element" id="NC_008261"/>
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189 <expand macro="zenodo_collection_element" id="NC_009012"/>
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190 <expand macro="zenodo_collection_element" id="NC_014168"/>
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191 <expand macro="zenodo_collection_element" id="NC_014212"/>
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192 <expand macro="zenodo_collection_element" id="NC_014364"/>
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193 <expand macro="zenodo_collection_element" id="NC_015761"/>
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194 <expand macro="zenodo_collection_element" id="NC_017033"/>
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195 <expand macro="zenodo_collection_element" id="NC_018068"/>
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196 <expand macro="zenodo_collection_element" id="NC_018515"/>
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197 <expand macro="zenodo_collection_element" id="NC_019936"/>
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198 <expand macro="zenodo_collection_element" id="NC_021184"/>
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199 <expand macro="zenodo_collection_element" id="NC_003450"/>
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200 <expand macro="zenodo_collection_element" id="NC_012982"/>
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201 <expand macro="zenodo_collection_element" id="NC_014008"/>
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202 <expand macro="zenodo_collection_element" id="NC_014211"/>
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203 <expand macro="zenodo_collection_element" id="NC_014363"/>
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204 <expand macro="zenodo_collection_element" id="NC_017095"/>
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205 <expand macro="zenodo_collection_element" id="NC_018014"/>
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206 <expand macro="zenodo_collection_element" id="NC_019897"/>
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207 <expand macro="zenodo_collection_element" id="NC_019904"/>
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208 </collection>
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209 </param>
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210 <param name="checkm" value="checkm2.Quality_report.tabular"/>
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211 <expand macro="test_collection" name="genomad" folder="genomad_virus_summary" ext="tabular"/>
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212 <expand macro="test_collection" name="genomad_phages" folder="genomad_virus_fasta" ext="fasta"/>
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213 <expand macro="test_collection" name="genomad_annotations" folder="genomad_virus_genes" ext="tabular"/>
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214 <expand macro="test_collection" name="defense_finder" folder="defense_finder_systems" ext="tabular"/>
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215 <param name="gtdb_summary" value="gtdbtk.bac120.summary"/>
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216 <expand macro="test_collection_non_empty" name="checkv" folder="checkv_quality_summary" ext="tabular"/>
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217 <expand macro="test_collection_non_empty" name="drep_compare" folder="drep_compare" ext="csv"/>
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218 <expand macro="test_collection_non_empty" name="drep_compare_clustering_dendrogram" folder="drep_compare_clustering_dendrogram" ext="pdf"/>
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219 <expand macro="test_collection_non_empty" name="iphop" folder="iphop_host_prediction_to_genome" ext="csv"/>
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220 <expand macro="test_collection_non_empty" name="abricate" folder="abricate_results" ext="tabular"/>
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221 <expand macro="test_collection_non_empty" name="vibrant" folder="vibrant_amg_individuals" ext="tabular"/>
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222 <output name="report">
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223 <assert_contents>
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224 <has_size min="100"/>
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225 <has_line line="&lt;html&gt;"/>
1
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226 <has_text text="Error: " negate="true"/>
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227 </assert_contents>
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228 </output>
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229 </test>
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230
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231 <!-- test with collection element identifiers contain suffix .fasta
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232 also GTDBTk and CheckM2 output tables contain the .fasta suffix-->
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233 <test>
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234 <param name="genomes">
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235 <collection type="list">
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236 <expand macro="zenodo_collection_element" id="NC_000913" suffix=".fasta"/>
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237 <expand macro="zenodo_collection_element" id="NC_002737" suffix=".fasta"/>
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238 <expand macro="zenodo_collection_element" id="NC_008261" suffix=".fasta"/>
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239 <expand macro="zenodo_collection_element" id="NC_009012" suffix=".fasta"/>
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240 <expand macro="zenodo_collection_element" id="NC_014168" suffix=".fasta"/>
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241 <expand macro="zenodo_collection_element" id="NC_014212" suffix=".fasta"/>
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242 <expand macro="zenodo_collection_element" id="NC_014364" suffix=".fasta"/>
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243 <expand macro="zenodo_collection_element" id="NC_015761" suffix=".fasta"/>
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244 <expand macro="zenodo_collection_element" id="NC_017033" suffix=".fasta"/>
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245 <expand macro="zenodo_collection_element" id="NC_018068" suffix=".fasta"/>
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246 <expand macro="zenodo_collection_element" id="NC_018515" suffix=".fasta"/>
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247 <expand macro="zenodo_collection_element" id="NC_019936" suffix=".fasta"/>
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248 <expand macro="zenodo_collection_element" id="NC_021184" suffix=".fasta"/>
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249 <expand macro="zenodo_collection_element" id="NC_003450" suffix=".fasta"/>
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250 <expand macro="zenodo_collection_element" id="NC_012982" suffix=".fasta"/>
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251 <expand macro="zenodo_collection_element" id="NC_014008" suffix=".fasta"/>
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252 <expand macro="zenodo_collection_element" id="NC_014211" suffix=".fasta"/>
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253 <expand macro="zenodo_collection_element" id="NC_014363" suffix=".fasta"/>
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254 <expand macro="zenodo_collection_element" id="NC_017095" suffix=".fasta"/>
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255 <expand macro="zenodo_collection_element" id="NC_018014" suffix=".fasta"/>
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256 <expand macro="zenodo_collection_element" id="NC_019897" suffix=".fasta"/>
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257 <expand macro="zenodo_collection_element" id="NC_019904" suffix=".fasta"/>
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258 </collection>
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259 </param>
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260 <param name="checkm" value="checkm2.Quality_report-wext.tabular"/>
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261 <expand macro="test_collection" name="genomad" suffix=".fasta" folder="genomad_virus_summary" ext="tabular"/>
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262 <expand macro="test_collection" name="genomad_phages" suffix=".fasta" folder="genomad_virus_fasta" ext="fasta"/>
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263 <expand macro="test_collection" name="genomad_annotations" suffix=".fasta" folder="genomad_virus_genes" ext="tabular"/>
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264 <expand macro="test_collection" name="defense_finder" suffix=".fasta" folder="defense_finder_systems" ext="tabular"/>
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265 <param name="gtdb_summary" value="gtdbtk.bac120-wext.summary"/>
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266 <expand macro="test_collection_non_empty" name="checkv" suffix=".fasta" folder="checkv_quality_summary" ext="tabular"/>
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267 <expand macro="test_collection_non_empty" name="drep_compare" suffix=".fasta" folder="drep_compare" ext="csv"/>
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268 <expand macro="test_collection_non_empty" name="drep_compare_clustering_dendrogram" suffix=".fasta" folder="drep_compare_clustering_dendrogram" ext="pdf"/>
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269 <expand macro="test_collection_non_empty" name="iphop" suffix=".fasta" folder="iphop_host_prediction_to_genome" ext="csv"/>
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270 <!-- TODO remove from test-data <expand macro="test_collection_non_empty" name="phatyp" folder="phabox_phatyp" ext="tabular"/> -->
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271 <expand macro="test_collection_non_empty" name="abricate" suffix=".fasta" folder="abricate_results" ext="tabular"/>
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272 <expand macro="test_collection_non_empty" name="vibrant" suffix=".fasta" folder="vibrant_amg_individuals" ext="tabular"/>
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273 <output name="report">
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274 <assert_contents>
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275 <has_size min="100"/>
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276 <has_line line="&lt;html&gt;"/>
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277 <has_text text="Error: " negate="true"/>
0
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278 </assert_contents>
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279 </output>
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280 </test>
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281 </tests>
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282 <help><![CDATA[
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283
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284 .. class:: infomark
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285
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286 **What it does**
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287
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288 Create a report for the PHI toolkit workflow.
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289
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290 Usage
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291 .....
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292
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293 **Input**
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294
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295 - Genomes
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296 - Checkm2 quality report
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297 - geNomad Virus Summary
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298 - geNomad Virus genes
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299 - DefenseFinder systems
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300 - GTDB-Tk summary
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301 - CheckV Quality summary
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302 - drep compare Cdb.csv
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303 - drep compare clustering dendrogram
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304 - iPHop Host prediction to genome
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305 - Abricate results
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306 - Vibrant Individual predicted virus AMGs
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307
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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308 **Output**
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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309
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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310 A html report summarizing the results.
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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311 ]]></help>
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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312 <!-- <citations>
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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313 <citation type="doi"> </citation>
315c2ed31af1 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 45c746567f48e6c9bcc19ba4e94e87348df3ac7a
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314 </citations> -->
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3a7f73d638ba planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phi-toolkit commit 368e8a7322c9763c648637263d4695abc146be13
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315 </tool>