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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 1d8e2a062d5138c843e4980c94a6c91a37146416
author iuc
date Tue, 03 Jun 2025 08:24:32 +0000
parents ff07b7d62944
children
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ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
iuc
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1 <?xml version="1.0"?>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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2 <tool id="omark" name="OMArk" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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3 <description>proteome quality assessment</description>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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4 <macros>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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5 <import>macros.xml</import>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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6 </macros>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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7 <xrefs>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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8 <xref type="bio.tools">omark</xref>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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9 </xrefs>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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10 <requirements>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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11 <expand macro="requirements" />
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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12 </requirements>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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13
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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14 <command detect_errors="exit_code"><![CDATA[
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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15 omamer search --db '$database.fields.path' --query '$input' --out 'output_omamer'
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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17 &&
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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19 omark
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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20 -f 'output_omamer'
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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21 -d '$database.fields.path'
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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22 $omark_mode
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ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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24 #if $input_iso:
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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25 -i '$input_iso'
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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26 #end if
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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27
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28 #if $t:
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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29 -t '$t'
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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30 #end if
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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31
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32 #if $r:
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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33 -r '$r'
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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34 #end if
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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35
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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36 -o omark_galaxy
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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37 ]]></command>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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38
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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39 <inputs>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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40 <param name="input" type="data" format="fasta" label="Protein sequences"/>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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41 <param name="input_iso" type="data" format="txt" optional="true" label="Input isoform file" help="A semi-colon separated file, listing all isoforms of each genes, with one gene per line."/>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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42 <param argument="-c" name="omark_mode" type="boolean" checked="false" truevalue="-c" falsevalue="" label="Only compute a list of conserved HOGs" help="Can be used to obtain a set of genes on which to train"/>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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43 <param name="database" label="OMAmer database" type="select">
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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44 <options from_data_table="omamer"/>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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45 </param>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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46
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47 <param argument="-t" type="text" optional="true" label="Taxonomic identifier" help="NCBI taxid corresponding to the input proteome">
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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48 <sanitizer invalid_char="">
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49 <valid initial="string.letters,string.digits">
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50 <add value="_" />
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51 </valid>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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52 </sanitizer>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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53 <validator type="regex">[0-9a-zA-Z_]+</validator>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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54 </param>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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55 <param argument="-r" type="text" optional="true" label="Taxonomic rank">
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56 <sanitizer invalid_char="">
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57 <valid initial="string.letters,string.digits">
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58 <add value="_" />
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59 </valid>
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60 </sanitizer>
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61 <validator type="regex">[0-9a-zA-Z_]+</validator>
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62 </param>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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63
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64 <param name="outputs" type="select" multiple="true" label="Which outputs should be generated">
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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65 <option value="detail_sum" selected="true">Detailed summary</option>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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66 <option value="hog">HOG identifiers</option>
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67 <option value="pdf">PDF Graphic representation </option>
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68 <option value="png">PNG Graphic representation </option>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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69 <option value="sum">Comparative proteome analysis</option>
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70 <option value="tax">Taxomony</option>
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71 <option value="ump">Protein identifiers</option>
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72 </param>
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73 </inputs>
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74
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75 <outputs>
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76 <data name="omark_detail_sum" format="txt" label="${tool.name} on ${on_string}: Detailed summary" from_work_dir="omark_galaxy/*detailed_summary.txt">
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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77 <filter>outputs and 'detail_sum' in outputs</filter>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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78 </data>
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79 <data name="omark_hog" format="omq" label="${tool.name} on ${on_string}: HOG identifiers" from_work_dir="omark_galaxy/*.omq">
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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80 <filter>outputs and 'hog' in outputs</filter>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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81 </data>
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82 <data name="omark_pdf" format="pdf" label="${tool.name} on ${on_string}: Graphic representation (pdf)" from_work_dir="omark_galaxy/*.pdf">
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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83 <filter>outputs and 'pdf' in outputs</filter>
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84 </data>
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85 <data name="omark_png" format="png" label="${tool.name} on ${on_string}: Graphic representation (png)" from_work_dir="omark_galaxy/*.png">
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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86 <filter>outputs and 'png' in outputs</filter>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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87 </data>
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88 <data name="omark_sum" format="sum" label="${tool.name} on ${on_string}: Comparative proteome analysis" from_work_dir="omark_galaxy/*.sum">
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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89 <filter>outputs and 'sum' in outputs</filter>
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90 </data>
ff07b7d62944 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/omark/ commit 547a79caaf320c241b148f73452036850880ce6f
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91 <data name="omark_tax" format="txt" label="${tool.name} on ${on_string}: Taxomony" from_work_dir="omark_galaxy/*.tax">
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92 <filter>outputs and 'tax' in outputs</filter>
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93 </data>
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94 <data name="omark_ump" format="ump" label="${tool.name} on ${on_string}: Protein identifiers" from_work_dir="omark_galaxy/*.ump">
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95 <filter>outputs and 'ump' in outputs</filter>
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96 </data>
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97 </outputs>
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98
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99 <tests>
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100 <test expect_failure="true">
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101 <param name="input" value="input.fasta"/>
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102 <param name="outputs" value="sum,detail_sum,png,hog,pdf,ump,tax"/>
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103 <param name="database" value="test"/>
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104
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105 <!-- Couldn't create a minimal working hdf5 dataset -->
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106 <assert_stderr>
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107 <has_text text="file signature not found"/>
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108 <has_text text="End of HDF5 error back trace" />
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109 </assert_stderr>
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110 </test>
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111 </tests>
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112
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113
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114 <help><![CDATA[
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115 OMark_: is a software for proteome quality assessment.
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116 It provides measures of proteome completeness, characterizes the consistency
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117 of all protein coding genes with regard to their homologs, and identifies the
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118 presence of contamination from other species.
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119
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120 OMArk relies on the OMA orthology database.
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121 For more information, please refer to the OMamer_ documentaion.
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122
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123 .. _OMark: https://github.com/DessimozLab/OMArk
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124 .. _OMamer: https://github.com/DessimozLab/omamer
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125 ]]></help>
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126 <expand macro="citation"/>
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127 </tool>