Mercurial > repos > iuc > prot_scriber

annotate prot-scriber.xml @ 3:ed4a6c9786c8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 6b50408a1ff7902575be37b2fa21aa80fe684e5c
author iuc
date Mon, 19 Aug 2024 06:47:18 +0000
parents c32f98757c4d
children
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278aa57e2c4d 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">
3
ed4a6c9786c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 6b50408a1ff7902575be37b2fa21aa80fe684e5c
iuc
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2 <description>Protein annotation of short human readable descriptions</description>
ed4a6c9786c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 6b50408a1ff7902575be37b2fa21aa80fe684e5c
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3 <macros>
ed4a6c9786c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 6b50408a1ff7902575be37b2fa21aa80fe684e5c
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4 <token name="@TOOL_VERSION@">0.1.6</token>
ed4a6c9786c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 6b50408a1ff7902575be37b2fa21aa80fe684e5c
iuc
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5 </macros>
ed4a6c9786c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 6b50408a1ff7902575be37b2fa21aa80fe684e5c
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6 <requirements>
ed4a6c9786c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 6b50408a1ff7902575be37b2fa21aa80fe684e5c
iuc
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7 <requirement type="package" version="@TOOL_VERSION@">prot-scriber</requirement>
ed4a6c9786c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 6b50408a1ff7902575be37b2fa21aa80fe684e5c
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8 </requirements>
ed4a6c9786c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 6b50408a1ff7902575be37b2fa21aa80fe684e5c
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9 <stdio>
ed4a6c9786c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 6b50408a1ff7902575be37b2fa21aa80fe684e5c
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10 <regex match="panicked" level="fatal" source="stderr"/>
ed4a6c9786c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 6b50408a1ff7902575be37b2fa21aa80fe684e5c
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11 </stdio>
ed4a6c9786c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 6b50408a1ff7902575be37b2fa21aa80fe684e5c
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12 <command>
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13 <![CDATA['prot-scriber'
278aa57e2c4d 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"
278aa57e2c4d 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 $input_config.seq_sim_table
278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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16 -s '$sst'
278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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17 #end for
278aa57e2c4d 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"
278aa57e2c4d 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 $input_config.advanced_input_repeat
278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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20 -s '$ssr.seq_sim_table'
278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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21 #if $ssr.header
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22 -e '$ssr.header'
2
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23 #else
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24 -e 'default'
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278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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25 #end if
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26 #if $ssr.field_separator
278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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27 -p '$ssr.field_separator'
2
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28 #else
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29 -p 'default'
0
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30 #end if
278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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31 #if $ssr.blacklist_regexs
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32 -b '$ssr.blacklist_regexs'
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33 #else
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34 -b 'default'
0
278aa57e2c4d 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 #if $ssr.capture_replace_pairs
278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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37 -c '$ssr.capture_replace_pairs'
2
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38 #else
c32f98757c4d 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
278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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40 #end if
278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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41 #if $ssr.filter_regexs
278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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42 -l '$ssr.filter_regexs'
2
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43 #else
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44 -l 'default'
0
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45 #end if
278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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46 #end for
278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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47 #if $input_config.expert_options.non_informative_words_regexs
278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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48 -w '$input_config.expert_options.non_informative_words_regexs'
278aa57e2c4d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23
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49 #end if
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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'
c32f98757c4d 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'
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62 #end if
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63 #if $seq_family.annotate_non_family_queries
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64 -a
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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'
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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>
3
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78 <inputs>
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79 <conditional name="input_config">
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80 <param name="input_config_selector" type="select" 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 name="seq_sim_table" argument="-s" type="data" 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. Required columns are: 'qacc sacc stitle' (Blast) or 'qseqid sseqid stitle' (Diamond)." multiple="true"/>
ed4a6c9786c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 6b50408a1ff7902575be37b2fa21aa80fe684e5c
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86 </when>
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87 <when value="advanced">
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88 <repeat name="advanced_input_repeat" title="Sequence similarity table" min="1" default="1">
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89 <param name="seq_sim_table" argument="-s" type="data" 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. Required columns are: 'qacc sacc stitle' (Blast) or 'qseqid sseqid stitle' (Diamond)."/>
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90 <param name="field_separator" argument="-p" type="text" optional="true" 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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91 <sanitizer>
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92 <valid initial="default">
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93 <add preset="string.printable"/>
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94 </valid>
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95 </sanitizer>
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96 </param>
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97 <param name="header" argument="-e" type="text" optional="true" label="Header of the sequence similarity tables (-e)" help="Header of the (-s) sequence similarity table. Separated by space (' ') the names of the 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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98 <param name="blacklist_regexs" argument="-b" type="data" format="tabular" optional="true" label="Blacklist Regexs (-b)" help="A file with regular expressions, one per line. Any match to any of these 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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99 <param name="capture_replace_pairs" argument="-c" type="data" format="tabular" optional="true" label="Capture replace pairs (-c)" help="A file with pairs of lines. Within each pair the first line is a regular expressions 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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100 <param name="filter_regexs" argument="-l" type="data" format="tabular" optional="true" label="Filter regexs (-l)" help="A file with regular expressions, one per line. Any match to any of these 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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101 </repeat>
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102 <section title="Expert options" name="expert_options">
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103 <param name="non_informative_words_regexs" argument="-w" type="data" format="tabular" optional="true" label="Non informative words regexs (-w)" help="A file in which regular expressions (regexs) are stored, one per line. These 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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104 <param name="description_split_regex" argument="-r" type="text" optional="true" label="Description split regex (-r)" help="A regular expression to be used to split descriptions (`stitle` in Blast terminology) into words. Default is '([~_\-/|\;,':.\s]+)'.">
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105 <sanitizer>
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106 <valid initial="default">
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107 <add preset="string.printable"/>
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108 </valid>
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109 </sanitizer>
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110 </param>
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111 <param name="center_inverse_word_information_content_at_quantile" argument="-q" type="integer" optional="true" label="Center inverse word-information-content at quantile (-q)" help="The quantile (percentile) to be subtracted from calculated inverse word information content to center these values. Value between 0 and 1."/>
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112 <param name="polish_capture_replace_pairs" argument="-d" type="data" format="txt" optional="true" label="Polishing capture replace pairs (-d)" help="A file with pairs of lines. Defines pairs of regex / replace pairs for post polishing of annotation results. Set to 'none' or provide an empty file to supress polishing."/>
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113 </section>
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114 </when>
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115 </conditional>
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116 <section title="Sequence family annotation" name="seq_family">
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117 <param name="seq_families" argument="-f" type="data" format="tabular" optional="true" label="Families of biological sequences (-f)" help="A file in which families of biological sequences are stored, one family per line. Each line must have format 'fam_name TAB gene1,gene2,gene3'. Make sure no gene appears in more than one family."/>
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118 <param name="annotate_non_family_queries" argument="-a" type="boolean" optional="true" 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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119 <param name="seq_family_gene_ids_separator" argument="-g" type="text" optional="true" label="Sequence family file gene-id separator (-g)" help=" A regular expression used to split the list of gene_identifiers in the argument --seq-families (-f) gene families file. Default is '(\s*,\s*|\s+)'.">
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120 <sanitizer>
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121 <valid initial="default">
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122 <add preset="string.printable"/>
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123 </valid>
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124 </sanitizer>
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125 </param>
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126 <param name="seq_family_id_genes_separator" argument="-i" type="text" optional="true" 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 string separates the gene_family_identifier (name) from the gene_identifier list that family comprises. Default is 'TAB'.">
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127 <sanitizer>
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128 <valid initial="default">
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129 <add preset="string.printable"/>
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130 </valid>
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131 </sanitizer>
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132 </param>
0
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133 </section>
3
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134 <param name="exclude_not_annotated_queries" argument="-x" type="boolean" optional="true" label="Exclude not annotated query sequences (-x)" help="Use this option to exclude results from the output table that could not be annotated."/>
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135 </inputs>
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136 <outputs>
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137 <data format="tabular" name="output"/>
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138 </outputs>
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139 <tests>
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140 <test>
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141 <param name="input_config_selector" value="basic"/>
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142 <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_blastp.txt,8_Proteins_vs_Trembl_blastp.txt"/>
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143 <output name="output" file="8_Proteins_prot-scriber.out" sort="true"/>
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144 </test>
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145 <test>
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146 <param name="input_config_selector" value="advanced"/>
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147 <repeat name="advanced_input_repeat">
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148 <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_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 <repeat name="advanced_input_repeat">
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153 <param name="seq_sim_table" value="8_Proteins_vs_Trembl_blastp.txt"/>
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154 <param name="field_separator" value="default"/>
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155 <param name="header" value="qacc sacc stitle"/>
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156 </repeat>
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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="blacklist_regexs" value="blacklist_stitle_regexs.txt"/>
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164 </repeat>
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165 <repeat name="advanced_input_repeat">
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166 <param name="seq_sim_table" value="8_Proteins_vs_Trembl_blastp.txt"/>
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167 <param name="blacklist_regexs" value="blacklist_stitle_regexs.txt"/>
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168 </repeat>
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169 <param name="description_split_regex" value="([~_\-/|;,'\'':.\s]+)"/>
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170 <param name="center_inverse_word_information_content_at_quantile" value="50"/>
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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 </tests>
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174 <help>
0
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175 <![CDATA[
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176
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177 **What it does**
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178
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179 prot-scriber_ assigns short human readable descriptions (HRD) to query biological sequences using reference candidate descriptions.
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180 In this, prot-scriber consumes sequence similarity search (Blast or Diamond or similar) results in tabular format.
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181 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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182 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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183
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184 .. _prot-scriber: http://github.com/usadellab/prot-scriber
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185 .. _README: https://github.com/usadellab/prot-scriber/blob/master/README.md
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186 .. _MANUAL: https://github.com/usadellab/prot-scriber/blob/master/README.md#manual
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187
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188 ----
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189
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190 **Input**
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191
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192 The input file is one or multiple tabular output(s) of a sequence similarity search (Blast, Diamon or similar).
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193 Required columns are: 'qacc sacc stitle' (Blast) or 'qseqid sseqid stitle' (Diamond). The input is done via the -s parameter::
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194
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195 -s, --seq-sim-table
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196 File in which to find sequence similarity search results in tabular format (SSST). Use
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197 e.g. Blast or Diamond to produce them. Required columns are: 'qacc sacc stitle' (Blast)
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198 or 'qseqid sseqid stitle' (Diamond). If the required columns, or more, appear in different order than
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199 shown here you must use the --header (-e) argument. If any of the input SSSTs uses a
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200 different field-separator than the '<TAB>' character, you must provide the --field-
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201 separator (-p) argument. You can provide multiple SSSTs for your query proteins whose information
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202 will be combined and evaluated by the tool.
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203
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204 **Input parameters**
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205
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206 prot-scriber gives the user the opportunity to fine tune parameters for the provided input tables.
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207 To do so turn on the *input configuration* switch. Those are optional, as the tool also provides sensible defaults.
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208 In case you decide to customize your inputs using below parameters, be advised that prot-scriber expects the
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209 customized parameter for all input tables - the number of tables and e.g. *--header* parameters have to match.
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210 You can set the values to 'default' if you want to use the default value for a given input table::
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211
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212 -e, --header
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213 Header of the --seq-sim-table (-s) arg. Separated by space (' ') the names of the
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214 columns in order of appearance in the respective table. Required and default columns are
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215 'qacc sacc stitle'. Note that this option only understands Blast terminology, i.e. even
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216 if you ran Diamond, please provide 'qacc' instead of 'qseqid' and 'sacc' instead of
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217 'sseqid'. Luckily 'stitle' is 'stitle' in Diamond, too. You can have additional columns
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218 that will be ignored, as long as the required columns appear in the correct order.
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219 Consider this example: 'qacc sacc evalue bitscore stitle'. Set to 'default' to use the hard coded default.
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220
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221 -p, --field-separator
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222 Field-Separator of the --seq-sim-table (-s) arg. The default value is the '<TAB>' character.
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223 Consider this example: ','. You can provide 'default' to use the hard coded default (TAB).
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224
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225 -b, --blacklist-regexs (Expert option)
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226 A file with regular expressions, one per line. Any match to any of these
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227 regular expressions causes sequence similarity search result descriptions ('stitle' in
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228 Blast terminology) to be discarded from the prot-scriber annotation process. Set to 'default' to use the hard
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229 coded default. An example file can be downloaded here:
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230 https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/blacklist_stitle_regexs.txt.
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231
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232 -l, --filter-regexs (Expert option)
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233 A file with regular expressions, one per line. Any match to any of these
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234 regular expressions causes the matched sub-string to be deleted, i.e. filtered out.
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235 Filtering is used to process descriptions ('stitle' in Blast terminology) and prepare
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236 the descriptions for the prot-scriber annotation process. In case of UniProt sequence
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237 similarity search results (Blast result tables), this removes the Blast Hit identifier
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238 (`sacc`) from the description (`stitle`) and also removes the taxonomic information
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239 starting with e.g. 'OS=' at the end of the `stitle` strings. Set to 'default' to use
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240 hard coded default. Anexample file can be downloaded here:
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241 https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/filter_stitle_regexs.txt.
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242
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243 -c, --capture-replace-pairs (Expert option)
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244 A file with pairs of lines. Within each pair the first line is a regular expressions
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245 defining one or more capture groups. The second line of a pair is the
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246 string used to replace the match in the regular expression with. This means the second
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247 line contains the capture groups. These pairs are used to further filter
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248 the sequence similarity search result descriptions ('stitle' in Blast terminology). In
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249 contrast to the --filter-regex (-l) matches are not deleted, but replaced with the
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250 second line of the pair. Filtering is used to process descriptions ('stitle' in Blast
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251 terminology) and prepare the descriptions for the prot-scriber annotation process.
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252 Set to 'default' to use the hard coded default. An example file can be downloaded here:
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253 https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/capture_replace_pairs.txt.
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254
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255 ----
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256
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257 **Gene family annotation**
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258
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259 prot-scriber can also apply the same methodology to produce HRDs for sets of biological sequences, i.e. gene families::
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260
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261 -f, --seq-families
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262 A file in which families of biological sequences are stored, one family per line. Each
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263 line must have format 'fam-name TAB gene1,gene2,gene3'. Make sure no gene appears in
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264 more than one family.
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265
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266 -g, --seq-family-gene-ids-separator
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267 A regular expression used to split the list of gene-identifiers in the
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268 argument --seq-families (-f) gene families file. Default is '(\s*,\s*|\s+)'.
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269
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270 -a, --annotate-non-family-queries
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271 Use this option only in combination with --seq-families (-f), i.e. when prot-scriber is
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272 used to generate human readable descriptions for gene families. If in that context this
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273 flag is given, queries for which there are sequence similarity search (Blast) results
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274 but that are NOT member of a sequence family will receive an annotation (human readable
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275 description) in the output file, too. Default value of this setting is 'OFF' (false).
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276
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277 ----
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278
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279 **Expert options**
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280
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281 Some additional optional configuration. Only use when you know what you are doing::
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282
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283 -w, --non-informative-words-regexs
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284 A file in which regular expressions (regexs) are stored, one per line. These
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285 regexs are used to recognize non-informative words, which will only receive a minimun
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286 score in the prot-scriber process that generates human readable description. There is a
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287 default list hard-coded into prot-scriber. An example file can be downloaded here:
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288 https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/non_informative_words_regexs.txt.
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289
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290 -r, --description-split-regex
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291 A regular expression to be used to split descriptions (`stitle` in Blast
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292 terminology) into words. Default is '([~_\-/|\;,':.\s]+)'.
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293
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294 -q, --center-inverse-word-information-content-at-quantile
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295 The quantile (percentile) to be subtracted from calculated inverse word information
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296 content to center these values. Consequently, this must be a value between zero and one
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297 or literal 50, which is interpreted as mean instead of a quantile. Default is 50,
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298 implying centering at the mean.
2
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299
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300 -d, --polish-capture-replace-pairs
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301 The last step of the process generating human readable descriptions (HRDs) for the
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302 queries (proteins or sequence families) is to 'polish' the selected HRDs. Polishing is
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303 done by iterative application of regular expressions (fancy-regex) and replace
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304 instructions (capture-replace-pairs). If you do not want to use the default polishing
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305 capture replace pairs specify a file in which pairs of lines are given. Of each pair the
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306 first line hold a regular expression (fancy-regex syntax) and the second the replacement
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307 instructions providing access to capture groups. Set to 'none' or provide an empty file,
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308 if you want to suppress polishing. If you want to have a template file for your custom
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309 polishing capture-replace-pairs please refer to
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310 https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/polish_capture_replace_pairs.txt
0
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311
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312 ----
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313
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314 **Output**
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315
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316 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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317
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318 Annotee-Identifier Human-Readable-Description
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319 Soltu.DM.02G020600.1 arath strubbelig receptor family
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320 Soltu.DM.S001650.1 germin member
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321 Soltu.DM.03G011280.1 increased dna methylation
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322 ...
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323
2
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324 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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325
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326 -x, --exclude-not-annotated-queries
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327 Exclude results from the output table that could not be annotated, i.e. 'unknown
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328 protein' or 'unknown sequence family', respectively.
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329
0
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330 ]]>
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331 </help>
3
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332 <citations>
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333 <citation type="bibtex">
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334 @misc{githubprot-scriber,
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335 author = {Asis Hallab},
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336 year = {2024},
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337 title = {prot-scriber},
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338 publisher = {Github},
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339 journal = {Github repository},
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340 url = {https://github.com/usadellab/prot-scriber},
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341 }</citation>
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342 </citations>
2
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343 </tool>