Mercurial > repos > iuc > prot_scriber

annotate prot-scriber.xml @ 2:4d4df9779b7b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit cbc2e768addc5b6697cdc4ed9b57bc7889a57fe9
author iuc
date Tue, 20 Sep 2022 09:45:46 +0000
parents 1e9a43cbf524
children 863ab6ebcafc
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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>
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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3 <macros>
2
4d4df9779b7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit cbc2e768addc5b6697cdc4ed9b57bc7889a57fe9
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4 <token name="@TOOL_VERSION@">0.1.4</token>
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5 </macros>
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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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" />
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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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'
2
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23 #else
4d4df9779b7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit cbc2e768addc5b6697cdc4ed9b57bc7889a57fe9
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24 -e 'default'
0
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25 #end if
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26 #if $ssr.field_separator
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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27 -p '$ssr.field_separator'
2
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28 #else
4d4df9779b7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit cbc2e768addc5b6697cdc4ed9b57bc7889a57fe9
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29 -p 'default'
0
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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30 #end if
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31 #if $ssr.blacklist_regexs
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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32 -b '$ssr.blacklist_regexs'
2
4d4df9779b7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit cbc2e768addc5b6697cdc4ed9b57bc7889a57fe9
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33 #else
4d4df9779b7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit cbc2e768addc5b6697cdc4ed9b57bc7889a57fe9
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34 -b 'default'
0
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35 #end if
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36 #if $ssr.capture_replace_pairs
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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37 -c '$ssr.capture_replace_pairs'
2
4d4df9779b7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit cbc2e768addc5b6697cdc4ed9b57bc7889a57fe9
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38 #else
4d4df9779b7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit cbc2e768addc5b6697cdc4ed9b57bc7889a57fe9
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39 -c 'default'
0
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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40 #end if
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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41 #if $ssr.filter_regexs
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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42 -l '$ssr.filter_regexs'
2
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43 #else
4d4df9779b7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit cbc2e768addc5b6697cdc4ed9b57bc7889a57fe9
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44 -l 'default'
0
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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 for
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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47 #if $input_config.expert_options.non_informative_words_regexs
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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48 -w '$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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49 #end if
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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50 #if $input_config.expert_options.description_split_regex
2
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51 -r '$input_config.expert_options.description_split_regex'
0
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52 #end if
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53 #if $input_config.expert_options.center_inverse_word_information_content_at_quantile
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54 -q $input_config.expert_options.center_inverse_word_information_content_at_quantile
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55 #end if
2
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56 #if $input_config.expert_options.polish_capture_replace_pairs
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57 -d '$input_config.expert_options.polish_capture_replace_pairs'
4d4df9779b7b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit cbc2e768addc5b6697cdc4ed9b57bc7889a57fe9
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58 #end if
0
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59 #end if
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60 #if $seq_family.seq_families
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61 -f '$seq_families'
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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62 #end if
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63 #if $seq_family.annotate_non_family_queries
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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64 -a
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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65 #end if
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66 #if $seq_family.seq_family_gene_ids_separator
2
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67 -g '$seq_family_gene_ids_separator'
0
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68 #end if
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69 #if $seq_family.seq_family_id_genes_separator
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70 -i '$seq_family_id_genes_separator'
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71 #end if
2
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72 #if $exclude_not_annotated_queries
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73 -x
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74 #end if
0
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75 -o '$output'
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76 ]]>
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77 </command>
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78 <inputs>
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79 <conditional name="input_config">
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80 <param type="select" name="input_config_selector" label="Choose input configuration options">
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81 <option value="basic" selected="true">Basic</option>
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82 <option value="advanced">Advanced</option>
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83 </param>
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84 <when value="basic">
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85 <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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86 Required columns are: 'qacc sacc stitle' (Blast) or 'qseqid sseqid stitle' (Diamond)." />
c840a1c77a0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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87 </when>
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88 <when value="advanced">
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89 <repeat name="advanced_input_repeat" title="Sequence similarity table" min="1" default="1">
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90 <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.
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91 Required columns are: 'qacc sacc stitle' (Blast) or 'qseqid sseqid stitle' (Diamond)." />
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92 <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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93 <sanitizer>
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94 <valid initial="default">
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95 <add preset="string.printable" />
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96 </valid>
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97 </sanitizer>
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98 </param>
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99 <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
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100 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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101 <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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102 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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103 <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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104 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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105 <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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106 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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107 </repeat>
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108 <section title="Expert options" name="expert_options">
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109 <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
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110 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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111 <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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112 terminology) into words. Default is '([~_\-/|\;,':.\s]+)'.">
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113 <sanitizer>
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114 <valid initial="default">
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115 <add preset="string.printable" />
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116 </valid>
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117 </sanitizer>
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118 </param>
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119 <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
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120 content to center these values. Value between 0 and 1." />
2
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121 <param type="data" optional="true" name="polish_capture_replace_pairs" argument="-d" label="Polishing capture replace pairs (-d)" help="A file with pairs of lines. Defines pairs of regex / replace
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122 pairs for post polishing of annotation results. Set to 'none' or provide an empty file to supress polishing."/>
0
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123 </section>
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124 </when>
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125 </conditional>
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126 <section title="Sequence family annotation" name="seq_family">
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127 <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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128 line must have format 'fam_name TAB gene1,gene2,gene3'. Make sure no gene appears in
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129 more than one family." />
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130 <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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131 <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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132 argument --seq-families (-f) gene families file. Default is '(\s*,\s*|\s+)'.">
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133 <sanitizer>
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134 <valid initial="default">
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135 <add preset="string.printable" />
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136 </valid>
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137 </sanitizer>
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138 </param>
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139 <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
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140 string separates the gene_family_identifier (name) from the gene_identifier list that family comprises. Default is 'TAB'.">
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141 <sanitizer>
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142 <valid initial="default">
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143 <add preset="string.printable" />
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144 </valid>
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145 </sanitizer>
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146 </param>
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147 </section>
2
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148 <param type="boolean" optional="true" name="exclude_not_annotated_queries" argument="-x" label="Exclude not annotated query sequences (-x)" help="Use this option to exclude results from the output table that could not be annotated."/>
0
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149 </inputs>
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150 <outputs>
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151 <data format="tabular" name="output" />
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152 </outputs>
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153 <tests>
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154 <test>
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155 <param name="input_config_selector" value="basic"/>
1
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156 <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_blastp.txt,8_Proteins_vs_Trembl_blastp.txt" />
0
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157 <output name="output" file="8_Proteins_prot-scriber.out" sort="true" />
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158 </test>
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159 <test>
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160 <param name="input_config_selector" value="advanced" />
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161 <repeat name="advanced_input_repeat">
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162 <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_blastp.txt" />
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163 <param name="field_separator" value="default" />
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164 <param name="header" value="qacc sacc stitle" />
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165 </repeat>
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166 <repeat name="advanced_input_repeat">
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167 <param name="seq_sim_table" value="8_Proteins_vs_Trembl_blastp.txt" />
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168 <param name="field_separator" value="default" />
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169 <param name="header" value="qacc sacc stitle" />
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170 </repeat>
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171 <output name="output" file="8_Proteins_prot-scriber.out" sort="true" />
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172 </test>
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173 <test>
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174 <param name="input_config_selector" value="advanced" />
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175 <repeat name="advanced_input_repeat">
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176 <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_blastp.txt" />
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177 <param name="blacklist_regexs" value="blacklist_stitle_regexs.txt" />
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178 </repeat>
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179 <repeat name="advanced_input_repeat">
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180 <param name="seq_sim_table" value="8_Proteins_vs_Trembl_blastp.txt" />
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181 <param name="blacklist_regexs" value="blacklist_stitle_regexs.txt" />
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182 </repeat>
2
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183 <param name="description_split_regex" value="([~_\-/|;,'\'':.\s]+)" />
0
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184 <param name="center_inverse_word_information_content_at_quantile" value="50" />
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185 <output name="output" file="8_Proteins_prot-scriber.out" sort="true" />
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186 </test>
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187 </tests>
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188 <help>
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189 <![CDATA[
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190
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191 **What it does**
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192
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193 prot-scriber_ assigns short human readable descriptions (HRD) to query biological sequences using reference candidate descriptions.
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194 In this, prot-scriber consumes sequence similarity search (Blast or Diamond or similar) results in tabular format.
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195 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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196 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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197
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198 .. _prot-scriber: http://github.com/usadellab/prot-scriber
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199 .. _README: https://github.com/usadellab/prot-scriber/blob/master/README.md
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200 .. _MANUAL: https://github.com/usadellab/prot-scriber/blob/master/README.md#manual
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201
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202 ----
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203
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204 **Input**
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205
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206 The input file is one or multiple tabular output(s) of a sequence similarity search (Blast, Diamon or similar).
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207 Required columns are: 'qacc sacc stitle' (Blast) or 'qseqid sseqid stitle' (Diamond). The input is done via the -s parameter::
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208
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209 -s, --seq-sim-table
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210 File in which to find sequence similarity search results in tabular format (SSST). Use
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211 e.g. Blast or Diamond to produce them. Required columns are: 'qacc sacc stitle' (Blast)
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212 or 'qseqid sseqid stitle' (Diamond). If the required columns, or more, appear in different order than
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213 shown here you must use the --header (-e) argument. If any of the input SSSTs uses a
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214 different field-separator than the '<TAB>' character, you must provide the --field-
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215 separator (-p) argument. You can provide multiple SSSTs for your query proteins whose information
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216 will be combined and evaluated by the tool.
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217
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218 **Input parameters**
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219
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220 prot-scriber gives the user the opportunity to fine tune parameters for the provided input tables.
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221 To do so turn on the *input configuration* switch. Those are optional, as the tool also provides sensible defaults.
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222 In case you decide to customize your inputs using below parameters, be advised that prot-scriber expects the
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223 customized parameter for all input tables - the number of tables and e.g. *--header* parameters have to match.
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224 You can set the values to 'default' if you want to use the default value for a given input table::
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225
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226 -e, --header
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227 Header of the --seq-sim-table (-s) arg. Separated by space (' ') the names of the
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228 columns in order of appearance in the respective table. Required and default columns are
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229 'qacc sacc stitle'. Note that this option only understands Blast terminology, i.e. even
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230 if you ran Diamond, please provide 'qacc' instead of 'qseqid' and 'sacc' instead of
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231 'sseqid'. Luckily 'stitle' is 'stitle' in Diamond, too. You can have additional columns
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232 that will be ignored, as long as the required columns appear in the correct order.
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233 Consider this example: 'qacc sacc evalue bitscore stitle'. Set to 'default' to use the hard coded default.
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234
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235 -p, --field-separator
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236 Field-Separator of the --seq-sim-table (-s) arg. The default value is the '<TAB>' character.
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237 Consider this example: ','. You can provide 'default' to use the hard coded default (TAB).
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238
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239 -b, --blacklist-regexs (Expert option)
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240 A file with regular expressions, one per line. Any match to any of these
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241 regular expressions causes sequence similarity search result descriptions ('stitle' in
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242 Blast terminology) to be discarded from the prot-scriber annotation process. Set to 'default' to use the hard
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243 coded default. An example file can be downloaded here:
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244 https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/blacklist_stitle_regexs.txt.
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245
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246 -l, --filter-regexs (Expert option)
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247 A file with regular expressions, one per line. Any match to any of these
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248 regular expressions causes the matched sub-string to be deleted, i.e. filtered out.
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249 Filtering is used to process descriptions ('stitle' in Blast terminology) and prepare
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250 the descriptions for the prot-scriber annotation process. In case of UniProt sequence
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251 similarity search results (Blast result tables), this removes the Blast Hit identifier
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252 (`sacc`) from the description (`stitle`) and also removes the taxonomic information
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253 starting with e.g. 'OS=' at the end of the `stitle` strings. Set to 'default' to use
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254 hard coded default. Anexample file can be downloaded here:
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255 https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/filter_stitle_regexs.txt.
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256
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257 -c, --capture-replace-pairs (Expert option)
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258 A file with pairs of lines. Within each pair the first line is a regular expressions
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259 defining one or more capture groups. The second line of a pair is the
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260 string used to replace the match in the regular expression with. This means the second
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261 line contains the capture groups. These pairs are used to further filter
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262 the sequence similarity search result descriptions ('stitle' in Blast terminology). In
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263 contrast to the --filter-regex (-l) matches are not deleted, but replaced with the
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264 second line of the pair. Filtering is used to process descriptions ('stitle' in Blast
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265 terminology) and prepare the descriptions for the prot-scriber annotation process.
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266 Set to 'default' to use the hard coded default. An example file can be downloaded here:
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267 https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/capture_replace_pairs.txt.
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268
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269 ----
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270
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271 **Gene family annotation**
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272
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273 prot-scriber can also apply the same methodology to produce HRDs for sets of biological sequences, i.e. gene families::
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274
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275 -f, --seq-families
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276 A file in which families of biological sequences are stored, one family per line. Each
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277 line must have format 'fam-name TAB gene1,gene2,gene3'. Make sure no gene appears in
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278 more than one family.
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279
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280 -g, --seq-family-gene-ids-separator
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281 A regular expression used to split the list of gene-identifiers in the
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282 argument --seq-families (-f) gene families file. Default is '(\s*,\s*|\s+)'.
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283
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284 -a, --annotate-non-family-queries
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285 Use this option only in combination with --seq-families (-f), i.e. when prot-scriber is
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286 used to generate human readable descriptions for gene families. If in that context this
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287 flag is given, queries for which there are sequence similarity search (Blast) results
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288 but that are NOT member of a sequence family will receive an annotation (human readable
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289 description) in the output file, too. Default value of this setting is 'OFF' (false).
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290
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291 ----
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292
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293 **Expert options**
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294
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295 Some additional optional configuration. Only use when you know what you are doing::
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296
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297 -w, --non-informative-words-regexs
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298 A file in which regular expressions (regexs) are stored, one per line. These
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299 regexs are used to recognize non-informative words, which will only receive a minimun
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300 score in the prot-scriber process that generates human readable description. There is a
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301 default list hard-coded into prot-scriber. An example file can be downloaded here:
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302 https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/non_informative_words_regexs.txt.
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303
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304 -r, --description-split-regex
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305 A regular expression to be used to split descriptions (`stitle` in Blast
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306 terminology) into words. Default is '([~_\-/|\;,':.\s]+)'.
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307
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308 -q, --center-inverse-word-information-content-at-quantile
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309 The quantile (percentile) to be subtracted from calculated inverse word information
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310 content to center these values. Consequently, this must be a value between zero and one
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311 or literal 50, which is interpreted as mean instead of a quantile. Default is 50,
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312 implying centering at the mean.
2
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313
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314 -d, --polish-capture-replace-pairs
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315 The last step of the process generating human readable descriptions (HRDs) for the
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316 queries (proteins or sequence families) is to 'polish' the selected HRDs. Polishing is
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317 done by iterative application of regular expressions (fancy-regex) and replace
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318 instructions (capture-replace-pairs). If you do not want to use the default polishing
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319 capture replace pairs specify a file in which pairs of lines are given. Of each pair the
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320 first line hold a regular expression (fancy-regex syntax) and the second the replacement
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321 instructions providing access to capture groups. Set to 'none' or provide an empty file,
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322 if you want to suppress polishing. If you want to have a template file for your custom
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323 polishing capture-replace-pairs please refer to
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324 https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/polish_capture_replace_pairs.txt
0
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325
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326 ----
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327
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328 **Output**
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329
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330 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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331
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332 Annotee-Identifier Human-Readable-Description
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333 Soltu.DM.02G020600.1 arath strubbelig receptor family
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334 Soltu.DM.S001650.1 germin member
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335 Soltu.DM.03G011280.1 increased dna methylation
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336 ...
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337
2
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338 If you want to supress results from the output table that could not be annotated, i.e. 'unknown protein' or 'unknown sequence family' respectively use the '-x' parameter::
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339
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340 -x, --exclude-not-annotated-queries
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341 Exclude results from the output table that could not be annotated, i.e. 'unknown
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342 protein' or 'unknown sequence family', respectively.
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343
0
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344 ]]>
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345 </help>
2
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346 </tool>