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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit bac22f562727babce8e0f456c82408c3063a683d |
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modified:
prot-scriber.xml test-data/8_Proteins_prot-scriber.out |
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| diff -r 4d4df9779b7b -r 863ab6ebcafc prot-scriber.xml --- a/prot-scriber.xml Tue Sep 20 09:45:46 2022 +0000 +++ b/prot-scriber.xml Sat May 18 20:36:38 2024 +0000 |
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| b'@@ -1,15 +1,15 @@\n <tool id="prot_scriber" name="prot-scriber" version="@TOOL_VERSION@" profile="21.05">\n- <description>Protein annotation of short human readable descriptions</description>\n- <macros>\n- <token name="@TOOL_VERSION@">0.1.4</token>\n- </macros>\n- <requirements>\n- <requirement type="package" version="@TOOL_VERSION@">prot-scriber</requirement>\n- </requirements>\n- <stdio>\n- <regex match="panicked" level="fatal" source="stderr" />\n- </stdio>\n- <command>\n+ <description>Protein annotation of short human readable descriptions</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">0.1.5</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">prot-scriber</requirement>\n+ </requirements>\n+ <stdio>\n+ <regex match="panicked" level="fatal" source="stderr"/>\n+ </stdio>\n+ <command>\n <![CDATA[\'prot-scriber\'\n #if str($input_config.input_config_selector) == "basic"\n #for $sst in $input_config.seq_sim_table\n@@ -75,117 +75,103 @@\n -o \'$output\'\n ]]>\n </command>\n- <inputs>\n- <conditional name="input_config">\n- <param type="select" name="input_config_selector" label="Choose input configuration options">\n- <option value="basic" selected="true">Basic</option>\n- <option value="advanced">Advanced</option>\n- </param>\n- <when value="basic">\n- <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.\n- Required columns are: \'qacc sacc stitle\' (Blast) or \'qseqid sseqid stitle\' (Diamond)." /> \n- </when>\n- <when value="advanced">\n- <repeat name="advanced_input_repeat" title="Sequence similarity table" min="1" default="1">\n- <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.\n- Required columns are: \'qacc sacc stitle\' (Blast) or \'qseqid sseqid stitle\' (Diamond)." /> \n- <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">\n- <sanitizer>\n- <valid initial="default">\n- <add preset="string.printable" />\n- </valid>\n- </sanitizer>\n- </param>\n- <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\n- 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" />\n- <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\n- 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" />\n- <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\n- 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'..b'ault" />\n- <param name="header" value="qacc sacc stitle" />\n- </repeat>\n- <repeat name="advanced_input_repeat">\n- <param name="seq_sim_table" value="8_Proteins_vs_Trembl_blastp.txt" />\n- <param name="field_separator" value="default" />\n- <param name="header" value="qacc sacc stitle" />\n- </repeat>\n- <output name="output" file="8_Proteins_prot-scriber.out" sort="true" />\n- </test>\n- <test>\n- <param name="input_config_selector" value="advanced" />\n- <repeat name="advanced_input_repeat">\n- <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_blastp.txt" />\n- <param name="blacklist_regexs" value="blacklist_stitle_regexs.txt" />\n- </repeat>\n- <repeat name="advanced_input_repeat">\n- <param name="seq_sim_table" value="8_Proteins_vs_Trembl_blastp.txt" />\n- <param name="blacklist_regexs" value="blacklist_stitle_regexs.txt" />\n- </repeat>\n- <param name="description_split_regex" value="([~_\\-/|;,\'\\\'\':.\\s]+)" />\n- <param name="center_inverse_word_information_content_at_quantile" value="50" />\n- <output name="output" file="8_Proteins_prot-scriber.out" sort="true" />\n- </test>\n- </tests>\n- <help>\n+ <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."/>\n+ </inputs>\n+ <outputs>\n+ <data format="tabular" name="output"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input_config_selector" value="basic"/>\n+ <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_blastp.txt,8_Proteins_vs_Trembl_blastp.txt"/>\n+ <output name="output" file="8_Proteins_prot-scriber.out" sort="true"/>\n+ </test>\n+ <test>\n+ <param name="input_config_selector" value="advanced"/>\n+ <repeat name="advanced_input_repeat">\n+ <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_blastp.txt"/>\n+ <param name="field_separator" value="default"/>\n+ <param name="header" value="qacc sacc stitle"/>\n+ </repeat>\n+ <repeat name="advanced_input_repeat">\n+ <param name="seq_sim_table" value="8_Proteins_vs_Trembl_blastp.txt"/>\n+ <param name="field_separator" value="default"/>\n+ <param name="header" value="qacc sacc stitle"/>\n+ </repeat>\n+ <output name="output" file="8_Proteins_prot-scriber.out" sort="true"/>\n+ </test>\n+ <test>\n+ <param name="input_config_selector" value="advanced"/>\n+ <repeat name="advanced_input_repeat">\n+ <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_blastp.txt"/>\n+ <param name="blacklist_regexs" value="blacklist_stitle_regexs.txt"/>\n+ </repeat>\n+ <repeat name="advanced_input_repeat">\n+ <param name="seq_sim_table" value="8_Proteins_vs_Trembl_blastp.txt"/>\n+ <param name="blacklist_regexs" value="blacklist_stitle_regexs.txt"/>\n+ </repeat>\n+ <param name="description_split_regex" value="([~_\\-/|;,\'\\\'\':.\\s]+)"/>\n+ <param name="center_inverse_word_information_content_at_quantile" value="50"/>\n+ <output name="output" file="8_Proteins_prot-scriber.out" sort="true"/>\n+ </test>\n+ </tests>\n+ <help>\n <![CDATA[\n \n **What it does**\n@@ -343,4 +329,15 @@\n \n ]]>\n </help>\n+ <citations>\n+ <citation type="bibtex">\n+ @misc{githubprot-scriber,\n+ author = {Asis Hallab},\n+ year = {2024},\n+ title = {prot-scriber},\n+ publisher = {Github},\n+ journal = {Github repository},\n+ url = {https://github.com/usadellab/prot-scriber},\n+ }</citation>\n+ </citations>\n </tool>\n' |
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| diff -r 4d4df9779b7b -r 863ab6ebcafc test-data/8_Proteins_prot-scriber.out --- a/test-data/8_Proteins_prot-scriber.out Tue Sep 20 09:45:46 2022 +0000 +++ b/test-data/8_Proteins_prot-scriber.out Sat May 18 20:36:38 2024 +0000 |
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| @@ -1,12 +1,12 @@ Annotee-Identifier Human-Readable-Description Soltu.DM.01G022510.1 sucrose nonfermenting protein x2 -Soltu.DM.02G020600.1 arath protein strubbelig receptor family +Soltu.DM.02G020600.1 protein strubbelig receptor family Soltu.DM.10G003150.1 sh and domain containing protein Soltu.DM.04G035790.1 phosphatidylinositol phosphatidylcholine transfer protein sfh Soltu.DM.02G015700.1 lrr receptor serine threonine protein kinase Soltu.DM.03G026010.1 arm repeat protein interacting with -Soltu.DM.07G016620.1 capch gdsl esterase lipase +Soltu.DM.07G016620.1 gdsl esterase lipase Soltu.DM.S001650.1 germin protein member Soltu.DM.03G011280.1 increased dna methylation -Soltu.DM.01G045390.1 gosmu hva protein +Soltu.DM.01G045390.1 hva protein Soltu.DM.09G022410.3 unknown protein |