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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/psortb commit 9275472791234aa6df4ed6e0e533bd9d74d83bdd
author bgruening
date Thu, 18 Dec 2025 16:15:09 +0000
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0
b97ecda36fc4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/psortb commit 9275472791234aa6df4ed6e0e533bd9d74d83bdd
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1 <tool id="psortb" name="PSORTb" version="3.0.6" profile="24.0">
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2 <description>Protein subcellular localization prediction for prokaryotes</description>
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3 <xrefs>
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4 <xref type="bio.tools">psortb</xref>
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5 </xrefs>
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6 <requirements>
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7 <container type="docker">quay.io/galaxy/psortb-cli:3.0.6</container>
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8 </requirements>
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9 <command detect_errors="exit_code">
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10 <![CDATA[
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11 mkdir \$TMPDIR/results &&
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12 /usr/local/psortb/bin/psort
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13 $gram.gram_choice
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14 #if $cutoff
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15 -c $cutoff
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16 #end if
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17 #if $divergent
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18 -d $divergent
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19 #end if
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20 -f fasta
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21 $exact
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22 -o $output_format
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23 -i $input_fasta
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24 &&
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25 mv \$TMPDIR/results/*_psortb_*.txt $output
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26 ]]>
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27 </command>
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28
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29 <inputs>
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30 <param name="input_fasta" type="data" format="fasta" label="Protein sequences (FASTA)" help="Submit protein sequences in FASTA format."/>
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31
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32 <section name="gram" title="Organism classification" expanded="true">
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33 <param name="gram_choice" type="select" label="Organism type">
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34 <option value="--positive" selected="true">Gram-positive (Bacteria)</option>
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35 <option value="--negative">Gram-negative (Bacteria)</option>
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36 <option value="--archaea">Archaea</option>
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37 </param>
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38 </section>
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39
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40 <param name="output_format" type="select" label="Output format" help="Choose PSORTb output format.">
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41 <option value="normal">Normal (human-readable)</option>
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42 <option value="terse">3-column (terse)</option>
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43 <option value="long" selected="true">30-column (long)</option>
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44 </param>
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45 <param argument="--exact" type="boolean" truevalue="--exact" falsevalue="" checked="false" label="Skip SCLBLASTe" help="Useful for batch runs of data against itself in SCLBLAST"/>
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46 <param argument="--cutoff" type="float" optional="true" label="Prediction cutoff" help="Sets a cutoff value for reported results (default: 7.5 used internally)."/>
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47 <param argument="--divergent" type="float" optional="true" label="Multiple localization cutoff" help="Sets a cutoff for flagging potential multiple localization sites."/>
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48 </inputs>
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49
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50 <outputs>
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51 <data name="output" format="txt" label="PSORTb results on ${on_string}"/>
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52 </outputs>
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53
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54 <tests>
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55 <test expect_num_outputs="1">
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56 <param name="input_fasta" value="psortb_pos.fa"/>
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57 <param name="gram|gram_choice" value="--positive"/>
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58 <param name="output_format" value="normal"/>
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59 <output name="output" value="psortb_pos_output.txt"/>
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60 </test>
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61 <test expect_num_outputs="1">
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62 <param name="input_fasta" value="psortb_neg.fa"/>
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63 <param name="gram|gram_choice" value="--negative"/>
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64 <param name="output_format" value="terse"/>
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65 <output name="output">
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66 <assert_contents>
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67 <has_text_matching expression="SeqID\tLocalization\tScore" />
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68 <has_text_matching expression="NP_949347\.1 \tUnknown\t7\.0" />
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69 </assert_contents>
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70 </output>
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71 </test>
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72 <test expect_num_outputs="1">
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73 <param name="input_fasta" value="psortb_arch.fa"/>
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74 <param name="gram|gram_choice" value="--archaea"/>
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75 <param name="output_format" value="long"/>
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76 <output name="output">
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77 <assert_contents>
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78 <has_text_matching expression="SeqID\s+CMSVM_a_Localization\s+CMSVM_a_Details\s+CWSVM_a_Localization\s+CWSVM_a_Details\s+CytoSVM_a_Localization\s+CytoSVM_a_Details\s+ECSVM_a_Localization\s+ECSVM_a_Details\s+ModHMM_a_Localization\s+ModHMM_a_Details\s+Motif_a_Localization\s+Motif_a_Details\s+Profile_a_Localization\s+Profile_a_Details\s+SCL-BLAST_a_Localization\s+SCL-BLAST_a_Details\s+SCL-BLASTe_a_Localization\s+SCL-BLASTe_a_Details\s+Signal_a_Localization\s+Signal_a_Details\s+Cytoplasmic_Score\s+CytoplasmicMembrane_Score\s+Cellwall_Score\s+Extracellular_Score\s+Final_Localization\s+Final_Localization_Details\s+Final_Score\s+Secondary_Localization\s+PSortb_Version" />
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79 <has_text_matching expression="YP_001689002\.1\s+Unknown\s+Unknown\s+Unknown\s+Extracellular\s+Unknown\s+1 internal helix found\s+Unknown\s+No motifs found\s+Unknown\s+No matches to profiles found\s+Extracellular\s+matched 47117675: Flagellin B1 precursor\s+Unknown\s+No matches against database\s+Unknown\s+No signal peptide detected\s+0.01\s+0.00\s+0.02\s+9.97\s+Extracellular\s+9.97\s+Flagellar\s+PSORTb version" />
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80 </assert_contents>
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81 </output>
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82 </test>
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83 </tests>
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84
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85 <help>
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86 <![CDATA[
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87 PSORTb predicts the subcellular localization of bacterial and archaeal proteins.
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88
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89 Input requirements
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90
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91 - Protein sequences in FASTA format. All sequences in one run should belong to the same organism class.
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92
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93 Options
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94
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95 - Organism type: select Gram-positive (`--positive`), Gram-negative (`--negative`), or Archaea (`--archaea`).
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96 - Output format: `normal` (human-readable), `terse` (tab-delimited), or `long` (tab-delimited with module details).
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97 - Cutoff (`-c`): threshold for final localization assignment (documentation suggests ~7.5).
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98 - Multiple localization cutoff (`-d`): threshold to flag possible multiple localization sites.
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99 - Exact (`--exact`): skip SCL-BLASTe step.
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100
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101 Notes
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102
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103 - PSORTb emphasizes precision; proteins with ambiguous signals may be reported as Unknown.
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104 - Long format includes module outputs and localization scores; terse/long are suitable for bulk processing.
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105
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106 Reference
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107
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108 https://psort.org/documentation/index.html
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109 ]]>
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110 </help>
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111
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112 <citations>
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113 <citation type="doi">10.1093/bioinformatics/btq249</citation>
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114 </citations>
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115 </tool>