Mercurial > repos > cpt > cpt_putative_usp

annotate generate-putative-usp.xml @ 1:f7afd1480d0f draft

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author cpt
date Mon, 05 Jun 2023 02:51:59 +0000
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1 <tool id="edu.tamu.cpt2.spanin.generate-putative-usp" name="USP Candidates" version="1.0">
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2 <description>constructs a putative list of potential u-spanin from an input genomic FASTA</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 <import>cpt-macros.xml</import>
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6 </macros>
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7 <expand macro="requirements">
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8 </expand>
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9 <command detect_errors="aggressive"><![CDATA[
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10 python '$__tool_directory__/generate-putative-usp.py'
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11 '$fa'
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12 --strand '$strand'
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13 --min_size '$min_size'
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14 --max_size '$max_size'
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15 --lipo_min_start '$lipo_min_start'
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16 --lipo_max_start '$lipo_max_start'
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17 --min_lipo_after '$min_lipo_after'
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18 --max_lipo_after '$max_lipo_after'
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19 --tmd_min_start '$tmd_min_start'
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20 --tmd_max_start '$tmd_max_start'
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21 --tmd_min_size '$tmd_min_size'
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22 --tmd_max_size '$tmd_max_size'
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23 --putative_usp_gff '$putative_usp_gff'
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24 --summary_usp_txt '$summary_usp'
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25 --putative_usp '$putative_usp'
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26 --usp_og '$usp_og'
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27 --usp_ob '$usp_ob'
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28 --usp_op '$usp_op'
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29 --usp_on '$usp_on'
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30 --switch '$switch'
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31 ]]></command>
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32 <inputs>
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33 <param label="FASTA" name="fa" type="data" format="fasta"/>
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34 <param type="select" label="Strand Choice" name="strand">
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35 <option value="both">both</option>
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36 <option value="forward">+</option>
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37 <option value="reverse">-</option>
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38 </param>
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39 <param label="u-spanin minimal length" type="integer" name="min_size" value="100"/>
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40 <param label="u-spanin maximum length" type="integer" name="max_size" value="200"/>
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41 <param label="Range Selection; default is all; slices are based on NT. Separated by a colon (eg. #:#)" name="switch" type="text" value="all"/>
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42 <param label="TMD minimal distance from start codon" type="integer" name="tmd_min_start" value="75"/>
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43 <param label="TMD maximum distance from start codon" type="integer" name="tmd_max_start" value="200"/>
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44 <param label="TMD minimal size" type="integer" name="tmd_min_size" value="15"/>
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45 <param label="TMD maximum size" type="integer" name="tmd_max_size" value="25"/>
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46 <param label="Lipobox minimal distance from start codon" type="integer" name="lipo_min_start" value="10"/>
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47 <param label="Lipobox maximum distance from start codon" type="integer" name="lipo_max_start" value="30"/>
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48 <param label="Minimum amount of periplasmic residues after Lipobox" type="integer" name="min_lipo_after" value="60"/>
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49 <param label="Maximum amount of periplasmic residues after Lipobox" type="integer" name="max_lipo_after" value="160"/>
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50 </inputs>
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51 <outputs>
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52 <data format="fasta" name="usp_on" label="NucSequences.fa" hidden="true"/>
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53 <data format="fasta" name="usp_op" label="ProtSequences.fa" hidden="true"/>
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54 <data format="bed" name="usp_ob" label="BED_Output.bed" hidden="true"/>
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55 <data format="gff3" name="usp_og" label="GFF_Output.gff" hidden="true"/>
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56 <data format="fasta" name="putative_usp" label="putative_usp.fa"/>
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57 <data format="txt" name="summary_usp" label="summary_usp.txt"/>
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58 <data format="gff3" name="putative_usp_gff" label="putative_usp.gff3"/>
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="fa" value="t1.fa"/>
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63 <param name="min-size" value="100"/>
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64 <param name="max-size" value="200"/>
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65 <param name="switch" value="all"/>
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66 <param name="tmd_min_start" value="75"/>
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67 <param name="tmd_max_start" value="200"/>
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68 <param name="tmd_min_size" value="15"/>
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69 <param name="tmd_max_size" value="25"/>
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70 <param name="lipo_min_start" value="15"/>
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71 <param name="lipo_max_start" value="30"/>
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72 <param name="min_lipo_after" value="60"/>
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73 <param name="max_lipo_after" value="160"/>
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74 <param name="select" value="1"/>
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75 <output name="usp_on" file="_out_usp.fna"/>
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76 <output name="usp_op" file="_out_usp.fa"/>
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77 <output name="usp_ob" file="_out_usp.bed"/>
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78 <output name="usp_og" file="_out_usp.gff3"/>
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79 <output name="putative_usp" file="_putative_usp.fa"/>
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80 <output name="summary_usp" file="_summary_usp.txt"/>
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81 <output name="putative_usp_gff" file="_putative_usp.gff3"/>
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82 </test>
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83 </tests>
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84 <help><![CDATA[
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85
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86 **What it does**
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87 Searches a genome for candidate u-spanins (USPs), a phage protein involved in outer membrane disruption during Gram-negative bacterial host cell lysis.
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88
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89
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90 **METHODOLOGY**
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91 This tool combines the methods used in the ISP and OSP Candidates tools to search for putative transmembrane domains and lipoboxes. See those tools for additional detail. Within user-set parameters, the following residues are allowed:
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92
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93 Hydrophobic residues allowed in TMD:
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94
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95 * [FIWLVMYCATGSP]
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96
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97 Lipobox patterns:
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98
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99 * [ILMFTV][^REKD][GAS]C
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100 * A W[AGS]C
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101
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102 **INPUT** --> Genomic FASTA
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103 *Note* - Use a single genome fasta. Multiple FASTAs will not work.
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104
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105 **OUTPUT** -->
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106 Protein sequences which passed the above filters are returned as the candidate USPs in three files: a protein FASTA file, a GFF3, and basic summary statistics text file.
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107 .
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108
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109 ]]></help>
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110 <citations>
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111 <citation type="doi">10.1371/journal.pcbi.1008214</citation>
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112 <citation type="doi">https://dx.doi.org/10.1016/bs.aivir.2018.09.003</citation>
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113 <citation type="bibtex">
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114 @unpublished{galaxyTools,
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115 author = {C. Ross},
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116 title = {CPT Galaxy Tools},
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117 year = {2020-},
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118 note = {https://github.com/tamu-cpt/galaxy-tools/}
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119 }
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120 </citation>
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121 </citations>
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122 </tool>