Mercurial > repos > iuc > prot_scriber

annotate prot-scriber.xml @ 1:1e9a43cbf524 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit ad83f6e032963de05c74bd65046e387715de2c6c
author iuc
date Wed, 15 Jun 2022 08:37:03 +0000
parents c840a1c77a0a
children 4d4df9779b7b
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c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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1 <tool id="prot_scriber" name="prot-scriber" version="@TOOL_VERSION@" profile="21.05">
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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2 <description>Protein annotation of short human readable descriptions</description>
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3 <macros>
1
1e9a43cbf524 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit ad83f6e032963de05c74bd65046e387715de2c6c
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4 <token name="@TOOL_VERSION@">0.1.3</token>
0
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">prot-scriber</requirement>
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8 </requirements>
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9 <stdio>
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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10 <regex match="panicked" level="fatal" source="stderr" />
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11 </stdio>
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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12 <command>
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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13 <![CDATA['prot-scriber'
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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14 #if str($input_config.input_config_selector) == "basic"
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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15 #for $sst in $input_config.seq_sim_table
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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16 -s '$sst'
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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17 #end for
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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18 #else if str($input_config.input_config_selector) == "advanced"
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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19 #for $ssr in $input_config.advanced_input_repeat
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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20 -s '$ssr.seq_sim_table'
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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21 #if $ssr.header
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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22 -e '$ssr.header'
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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23 #end if
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24 #if $ssr.field_separator
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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25 -p '$ssr.field_separator'
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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26 #end if
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27 #if $ssr.blacklist_regexs
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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28 -b '$ssr.blacklist_regexs'
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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29 #end if
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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30 #if $ssr.capture_replace_pairs
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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31 -c '$ssr.capture_replace_pairs'
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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32 #end if
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33 #if $ssr.filter_regexs
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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34 -l '$ssr.filter_regexs'
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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35 #end if
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36 #end for
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37 #if $input_config.expert_options.non_informative_words_regexs
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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38 -w '$input_config.expert_options.non_informative_words_regexs'
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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39 #end if
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40 #if $input_config.expert_options.description_split_regex
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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41 -r "$input_config.expert_options.description_split_regex"
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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42 #end if
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43 #if $input_config.expert_options.center_inverse_word_information_content_at_quantile
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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44 -q $input_config.expert_options.center_inverse_word_information_content_at_quantile
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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45 #end if
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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46 #end if
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47 #if $seq_family.seq_families
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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48 -f '$seq_families'
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49 #end if
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50 #if $seq_family.annotate_non_family_queries
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51 -a
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52 #end if
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53 #if $seq_family.seq_family_gene_ids_separator
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54 -g "$seq_family_gene_ids_separator"
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55 #end if
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56 #if $seq_family.seq_family_id_genes_separator
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57 -i '$seq_family_id_genes_separator'
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58 #end if
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59 -o '$output'
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60 ]]>
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61 </command>
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62 <inputs>
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63 <conditional name="input_config">
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64 <param type="select" name="input_config_selector" label="Choose input configuration options">
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65 <option value="basic" selected="true">Basic</option>
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66 <option value="advanced">Advanced</option>
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67 </param>
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68 <when value="basic">
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69 <param type="data" multiple="true" name="seq_sim_table" argument="-s" format="tabular" label="Sequence similarity search results in tabular format (-s)" help="Files in which to find sequence similarity search results in tabular format (SSST). Use e.g. Blast or Diamond to produce them.
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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70 Required columns are: 'qacc sacc stitle' (Blast) or 'qseqid sseqid stitle' (Diamond)." />
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71 </when>
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72 <when value="advanced">
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73 <repeat name="advanced_input_repeat" title="Sequence similarity table" min="1" default="1">
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74 <param type="data" name="seq_sim_table" argument="-s" format="tabular" label="Sequence similarity search result in tabular format (-s)" help="File in which to find sequence similarity search results in tabular format (SSST). Use e.g. Blast or Diamond to produce them.
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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75 Required columns are: 'qacc sacc stitle' (Blast) or 'qseqid sseqid stitle' (Diamond)." />
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76 <param type="text" optional="true" name="field_separator" argument="-p" label="Field separator (-p)" help="Field-Separator of the (-s) sequence similarity table. The default value is the 'TAB' character. Set to 'default' to use the hard coded default">
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77 <sanitizer>
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78 <valid initial="default">
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79 <add preset="string.printable" />
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80 </valid>
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81 </sanitizer>
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82 </param>
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83 <param type="text" optional="true" name="header" argument="-e" label="Header of the sequence similarity tables (-e)" help="Header of the (-s) sequence similarity table. Separated by space (' ') the names of the
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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84 in order of appearance in the respective table. Required and default columns are 'qacc sacc stitle'. Set to 'default' to use the hard coded default" />
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85 <param type="data" optional="true" name="blacklist_regexs" argument="-b" format="tabular" label="Blacklist Regexs (-b)" help="A file with regular expressions, one per line. Any match to any of these
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86 regular expressions causes sequence similarity search result descriptions ('stitle' in Blast terminology) to be discarded from the prot-scriber annotation process. Set to 'default' to use the hard coded default" />
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87 <param type="data" optional="true" name="capture_replace_pairs" argument="-c" format="tabular" label="Capture replace pairs (-c)" help="A file with pairs of lines. Within each pair the first line is a regular expressions
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88 defining one or more capture groups. The second line of a pair is the string used to replace the match in the regular expression with. Set to 'default' to use the hard coded default" />
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89 <param type="data" optional="true" name="filter_regexs" argument="-l" format="tabular" label="Filter regexs (-l)" help="A file with regular expressions, one per line. Any match to any of these
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90 regular expressions causes the matched sub-string to be deleted, i.e. filtered out. Set to 'default' to use the hard coded default" />
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91 </repeat>
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92 <section title="Expert options" name="expert_options">
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93 <param type="data" optional="true" name="non_informative_words_regexs" argument="-w" format="tabular" label="Non informative words regexs (-w)" help="A file in which regular expressions (regexs) are stored, one per line. These
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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94 regexs are used to recognize non-informative words, which will only receive a minimum score in the prot-scriber process that generates human readable description." />
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95 <param type="text" optional="true" name="description_split_regex" argument="-r" label="Description split regex (-r)" help="A regular expression to be used to split descriptions (`stitle` in Blast
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96 terminology) into words. Default is '([~_\-/|\;,':.\s]+)'.">
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97 <sanitizer>
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98 <valid initial="default">
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99 <add preset="string.printable" />
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100 </valid>
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101 </sanitizer>
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102 </param>
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103 <param type="integer" optional="true" name="center_inverse_word_information_content_at_quantile" argument="-q" label="Center inverse word-information-content at quantile (-q)" help="The quantile (percentile) to be subtracted from calculated inverse word information
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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104 content to center these values. Value between 0 and 1." />
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105 </section>
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106 </when>
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107 </conditional>
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108 <section title="Sequence family annotation" name="seq_family">
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109 <param type="data" optional="true" name="seq_families" argument="-f" format="tabular" label="Families of biological sequences (-f)" help="A file in which families of biological sequences are stored, one family per line. Each
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110 line must have format 'fam_name TAB gene1,gene2,gene3'. Make sure no gene appears in
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111 more than one family." />
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112 <param type="boolean" optional="true" name="annotate_non_family_queries" argument="-a" label="Annotate non family query sequences (-a)" help="Set this to true to also annotate sequences are not member of a sequence family." />
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113 <param type="text" optional="true" name="seq_family_gene_ids_separator" argument="-g" label="Sequence family file gene-id separator (-g)" help=" A regular expression used to split the list of gene_identifiers in the
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114 argument --seq-families (-f) gene families file. Default is '(\s*,\s*|\s+)'.">
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115 <sanitizer>
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116 <valid initial="default">
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117 <add preset="string.printable" />
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118 </valid>
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119 </sanitizer>
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120 </param>
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121 <param type="text" optional="true" name="seq_family_id_genes_separator" argument="-i" label="Sequence family file family - gene-id separator (-i)" help="A string used as separator in the argument --seq-families (-f) gene families file. This
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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122 string separates the gene_family_identifier (name) from the gene_identifier list that family comprises. Default is 'TAB'.">
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123 <sanitizer>
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124 <valid initial="default">
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125 <add preset="string.printable" />
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126 </valid>
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127 </sanitizer>
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128 </param>
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129 </section>
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130 </inputs>
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131 <outputs>
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132 <data format="tabular" name="output" />
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133 </outputs>
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134 <tests>
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135 <test>
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136 <param name="input_config_selector" value="basic"/>
1
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137 <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_blastp.txt,8_Proteins_vs_Trembl_blastp.txt" />
0
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138 <output name="output" file="8_Proteins_prot-scriber.out" sort="true" />
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139 </test>
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140 <test>
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141 <param name="input_config_selector" value="advanced" />
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142 <repeat name="advanced_input_repeat">
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143 <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_blastp.txt" />
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144 <param name="field_separator" value="default" />
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145 <param name="header" value="qacc sacc stitle" />
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146 </repeat>
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147 <repeat name="advanced_input_repeat">
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148 <param name="seq_sim_table" value="8_Proteins_vs_Trembl_blastp.txt" />
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149 <param name="field_separator" value="default" />
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150 <param name="header" value="qacc sacc stitle" />
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151 </repeat>
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152 <output name="output" file="8_Proteins_prot-scriber.out" sort="true" />
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153 </test>
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154 <test>
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155 <param name="input_config_selector" value="advanced" />
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156 <repeat name="advanced_input_repeat">
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157 <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_blastp.txt" />
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158 <param name="blacklist_regexs" value="blacklist_stitle_regexs.txt" />
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159 </repeat>
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160 <repeat name="advanced_input_repeat">
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161 <param name="seq_sim_table" value="8_Proteins_vs_Trembl_blastp.txt" />
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162 <param name="blacklist_regexs" value="blacklist_stitle_regexs.txt" />
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163 </repeat>
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164 <param name="description_split_regex" value="([~_\-/|;,':.\s]+)" />
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165 <param name="center_inverse_word_information_content_at_quantile" value="50" />
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166 <output name="output" file="8_Proteins_prot-scriber.out" sort="true" />
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167 </test>
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168 </tests>
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169 <help>
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170 <![CDATA[
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171
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172 **What it does**
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173
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174 prot-scriber_ assigns short human readable descriptions (HRD) to query biological sequences using reference candidate descriptions.
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175 In this, prot-scriber consumes sequence similarity search (Blast or Diamond or similar) results in tabular format.
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176 customized lexical analysis is carried out on the descriptions of these Blast Hits and a resulting HRD is assigned to the query sequences.
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177 For more information, examples and how to use the prot-scriber commandline tool refer to the prot-scriber README_ and MANUAL_.
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178
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179 .. _prot-scriber: http://github.com/usadellab/prot-scriber
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180 .. _README: https://github.com/usadellab/prot-scriber/blob/master/README.md
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181 .. _MANUAL: https://github.com/usadellab/prot-scriber/blob/master/README.md#manual
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182
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183 ----
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184
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185 **Input**
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186
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187 The input file is one or multiple tabular output(s) of a sequence similarity search (Blast, Diamon or similar).
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188 Required columns are: 'qacc sacc stitle' (Blast) or 'qseqid sseqid stitle' (Diamond). The input is done via the -s parameter::
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189
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190 -s, --seq-sim-table
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191 File in which to find sequence similarity search results in tabular format (SSST). Use
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192 e.g. Blast or Diamond to produce them. Required columns are: 'qacc sacc stitle' (Blast)
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193 or 'qseqid sseqid stitle' (Diamond). If the required columns, or more, appear in different order than
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194 shown here you must use the --header (-e) argument. If any of the input SSSTs uses a
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195 different field-separator than the '<TAB>' character, you must provide the --field-
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196 separator (-p) argument. You can provide multiple SSSTs for your query proteins whose information
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197 will be combined and evaluated by the tool.
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198
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199 **Input parameters**
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200
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201 prot-scriber gives the user the opportunity to fine tune parameters for the provided input tables.
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202 To do so turn on the *input configuration* switch. Those are optional, as the tool also provides sensible defaults.
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203 In case you decide to customize your inputs using below parameters, be advised that prot-scriber expects the
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204 customized parameter for all input tables - the number of tables and e.g. *--header* parameters have to match.
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205 You can set the values to 'default' if you want to use the default value for a given input table::
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206
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207 -e, --header
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208 Header of the --seq-sim-table (-s) arg. Separated by space (' ') the names of the
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209 columns in order of appearance in the respective table. Required and default columns are
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210 'qacc sacc stitle'. Note that this option only understands Blast terminology, i.e. even
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211 if you ran Diamond, please provide 'qacc' instead of 'qseqid' and 'sacc' instead of
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212 'sseqid'. Luckily 'stitle' is 'stitle' in Diamond, too. You can have additional columns
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213 that will be ignored, as long as the required columns appear in the correct order.
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214 Consider this example: 'qacc sacc evalue bitscore stitle'. Set to 'default' to use the hard coded default.
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215
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216 -p, --field-separator
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217 Field-Separator of the --seq-sim-table (-s) arg. The default value is the '<TAB>' character.
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218 Consider this example: ','. You can provide 'default' to use the hard coded default (TAB).
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219
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220 -b, --blacklist-regexs (Expert option)
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221 A file with regular expressions, one per line. Any match to any of these
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222 regular expressions causes sequence similarity search result descriptions ('stitle' in
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223 Blast terminology) to be discarded from the prot-scriber annotation process. Set to 'default' to use the hard
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224 coded default. An example file can be downloaded here:
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225 https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/blacklist_stitle_regexs.txt.
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226
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227 -l, --filter-regexs (Expert option)
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228 A file with regular expressions, one per line. Any match to any of these
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229 regular expressions causes the matched sub-string to be deleted, i.e. filtered out.
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230 Filtering is used to process descriptions ('stitle' in Blast terminology) and prepare
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231 the descriptions for the prot-scriber annotation process. In case of UniProt sequence
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232 similarity search results (Blast result tables), this removes the Blast Hit identifier
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233 (`sacc`) from the description (`stitle`) and also removes the taxonomic information
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234 starting with e.g. 'OS=' at the end of the `stitle` strings. Set to 'default' to use
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235 hard coded default. Anexample file can be downloaded here:
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236 https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/filter_stitle_regexs.txt.
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237
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238 -c, --capture-replace-pairs (Expert option)
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239 A file with pairs of lines. Within each pair the first line is a regular expressions
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240 defining one or more capture groups. The second line of a pair is the
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241 string used to replace the match in the regular expression with. This means the second
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242 line contains the capture groups. These pairs are used to further filter
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243 the sequence similarity search result descriptions ('stitle' in Blast terminology). In
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244 contrast to the --filter-regex (-l) matches are not deleted, but replaced with the
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245 second line of the pair. Filtering is used to process descriptions ('stitle' in Blast
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246 terminology) and prepare the descriptions for the prot-scriber annotation process.
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247 Set to 'default' to use the hard coded default. An example file can be downloaded here:
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248 https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/capture_replace_pairs.txt.
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249
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250 ----
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251
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252 **Gene family annotation**
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253
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254 prot-scriber can also apply the same methodology to produce HRDs for sets of biological sequences, i.e. gene families::
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255
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256 -f, --seq-families
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257 A file in which families of biological sequences are stored, one family per line. Each
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258 line must have format 'fam-name TAB gene1,gene2,gene3'. Make sure no gene appears in
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259 more than one family.
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260
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261 -g, --seq-family-gene-ids-separator
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262 A regular expression used to split the list of gene-identifiers in the
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263 argument --seq-families (-f) gene families file. Default is '(\s*,\s*|\s+)'.
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264
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265 -a, --annotate-non-family-queries
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266 Use this option only in combination with --seq-families (-f), i.e. when prot-scriber is
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267 used to generate human readable descriptions for gene families. If in that context this
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268 flag is given, queries for which there are sequence similarity search (Blast) results
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269 but that are NOT member of a sequence family will receive an annotation (human readable
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270 description) in the output file, too. Default value of this setting is 'OFF' (false).
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271
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272 ----
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273
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274 **Expert options**
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275
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276 Some additional optional configuration. Only use when you know what you are doing::
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277
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278 -w, --non-informative-words-regexs
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279 A file in which regular expressions (regexs) are stored, one per line. These
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280 regexs are used to recognize non-informative words, which will only receive a minimun
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281 score in the prot-scriber process that generates human readable description. There is a
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282 default list hard-coded into prot-scriber. An example file can be downloaded here:
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283 https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/non_informative_words_regexs.txt.
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284
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285 -r, --description-split-regex
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286 A regular expression to be used to split descriptions (`stitle` in Blast
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287 terminology) into words. Default is '([~_\-/|\;,':.\s]+)'.
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288
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289 -q, --center-inverse-word-information-content-at-quantile
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290 The quantile (percentile) to be subtracted from calculated inverse word information
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291 content to center these values. Consequently, this must be a value between zero and one
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292 or literal 50, which is interpreted as mean instead of a quantile. Default is 50,
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293 implying centering at the mean.
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294
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295 ----
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296
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297 **Output**
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298
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299 prot-scriber outputs a single tab-separated text file with the annotated sequences or gene-families, depending on how you ran the program, one result per line::
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300
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301 Annotee-Identifier Human-Readable-Description
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302 Soltu.DM.02G020600.1 arath strubbelig receptor family
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303 Soltu.DM.S001650.1 germin member
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304 Soltu.DM.03G011280.1 increased dna methylation
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305 ...
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306
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307 ]]>
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308 </help>
1
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309 </tool>