diff prot-scriber.xml @ 0:c840a1c77a0a draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prot-scriber commit 8b58f3f03d6430689d228029bb2eb46c16cfff23

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/prot-scriber.xml	Tue May 10 13:18:05 2022 +0000
@@ -0,0 +1,310 @@
+<tool id="prot_scriber" name="prot-scriber" version="@TOOL_VERSION@" profile="21.05">
+  <description>Protein annotation of short human readable descriptions</description>
+  <macros>
+    <token name="@TOOL_VERSION@">0.1.1</token>
+  </macros>
+  <requirements>
+    <requirement type="package" version="@TOOL_VERSION@">prot-scriber</requirement>
+  </requirements>
+  <stdio>
+    <regex match="panicked" level="fatal" source="stderr" />
+  </stdio>
+  <command>
+    <![CDATA['prot-scriber'
+    #if str($input_config.input_config_selector) == "basic"
+      #for $sst in $input_config.seq_sim_table
+        -s '$sst'
+      #end for
+    #else if str($input_config.input_config_selector) == "advanced"
+      #for $ssr in $input_config.advanced_input_repeat
+        -s '$ssr.seq_sim_table'
+        #if $ssr.header
+          -e '$ssr.header'
+        #end if
+        #if $ssr.field_separator
+          -p '$ssr.field_separator'
+        #end if
+        #if $ssr.blacklist_regexs
+          -b '$ssr.blacklist_regexs'
+        #end if
+        #if $ssr.capture_replace_pairs
+          -c '$ssr.capture_replace_pairs'
+        #end if
+        #if $ssr.filter_regexs
+          -l '$ssr.filter_regexs'
+        #end if
+      #end for   
+      #if $input_config.expert_options.non_informative_words_regexs
+        -w '$input_config.expert_options.non_informative_words_regexs'
+      #end if
+      #if $input_config.expert_options.description_split_regex
+        -r "$input_config.expert_options.description_split_regex"
+      #end if
+      #if $input_config.expert_options.center_inverse_word_information_content_at_quantile
+        -q $input_config.expert_options.center_inverse_word_information_content_at_quantile
+      #end if
+    #end if
+    #if $seq_family.seq_families
+      -f '$seq_families'
+    #end if
+    #if $seq_family.annotate_non_family_queries
+      -a
+    #end if
+    #if $seq_family.seq_family_gene_ids_separator
+      -g "$seq_family_gene_ids_separator"
+    #end if
+    #if $seq_family.seq_family_id_genes_separator
+      -i '$seq_family_id_genes_separator'
+    #end if
+    -o '$output'
+    ]]>
+  </command>
+  <inputs>
+    <conditional name="input_config">
+      <param type="select" name="input_config_selector" label="Choose input configuration options">
+        <option value="basic" selected="true">Basic</option>
+        <option value="advanced">Advanced</option>
+      </param>
+      <when value="basic">
+        <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.
+        Required columns are: 'qacc sacc stitle' (Blast) or 'qseqid sseqid stitle' (Diamond)." /> 
+      </when>
+      <when value="advanced">
+        <repeat name="advanced_input_repeat" title="Sequence similarity table" min="1" default="1">
+          <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.
+          Required columns are: 'qacc sacc stitle' (Blast) or 'qseqid sseqid stitle' (Diamond)." /> 
+          <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">
+            <sanitizer>
+              <valid initial="default">
+                <add preset="string.printable" />
+              </valid>
+            </sanitizer>
+          </param>
+          <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
+            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" />
+          <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
+            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" />
+          <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
+            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" />
+          <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
+            regular expressions causes the matched sub-string to be deleted, i.e. filtered out. Set to 'default' to use the hard coded default" /> 
+        </repeat>
+        <section title="Expert options" name="expert_options">
+          <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
+            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." />
+          <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
+            terminology) into words. Default is '([~_\-/|\;,':.\s]+)'.">
+            <sanitizer>
+              <valid initial="default">
+                <add preset="string.printable" />
+              </valid>
+            </sanitizer>
+          </param>
+          <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
+            content to center these values. Value between 0 and 1." />
+        </section>
+      </when>
+    </conditional>
+    <section title="Sequence family annotation" name="seq_family">
+      <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
+        line must have format 'fam_name TAB gene1,gene2,gene3'. Make sure no gene appears in
+        more than one family." />
+      <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." />
+      <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
+        argument --seq-families (-f) gene families file. Default is '(\s*,\s*|\s+)'.">
+        <sanitizer>
+          <valid initial="default">
+            <add preset="string.printable" />
+          </valid>
+        </sanitizer>
+      </param>
+      <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
+        string separates the gene_family_identifier (name) from the gene_identifier list that family comprises. Default is 'TAB'.">
+        <sanitizer>
+          <valid initial="default">
+            <add preset="string.printable" />
+          </valid>
+        </sanitizer>
+      </param>
+    </section>
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input_config_selector" value="basic"/>
+      <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_blastp.txt" />
+      <param name="seq_sim_table" value="8_Proteins_vs_Trembl_blastp.txt" />
+      <output name="output" file="8_Proteins_prot-scriber.out" sort="true" />
+    </test>
+    <test>
+      <param name="input_config_selector" value="advanced" />
+      <repeat name="advanced_input_repeat">
+        <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_blastp.txt" />
+        <param name="field_separator" value="default" />
+        <param name="header" value="qacc sacc stitle" />
+      </repeat>
+      <repeat name="advanced_input_repeat">
+        <param name="seq_sim_table" value="8_Proteins_vs_Trembl_blastp.txt" />
+        <param name="field_separator" value="default" />
+        <param name="header" value="qacc sacc stitle" />
+      </repeat>
+      <output name="output" file="8_Proteins_prot-scriber.out" sort="true" />
+    </test>
+    <test>
+      <param name="input_config_selector" value="advanced" />
+      <repeat name="advanced_input_repeat">
+        <param name="seq_sim_table" value="8_Proteins_vs_Swissprot_blastp.txt" />
+        <param name="blacklist_regexs" value="blacklist_stitle_regexs.txt" />
+      </repeat>
+      <repeat name="advanced_input_repeat">
+        <param name="seq_sim_table" value="8_Proteins_vs_Trembl_blastp.txt" />
+        <param name="blacklist_regexs" value="blacklist_stitle_regexs.txt" />
+      </repeat>
+      <param name="description_split_regex" value="([~_\-/|;,':.\s]+)" />
+      <param name="center_inverse_word_information_content_at_quantile" value="50" />
+      <output name="output" file="8_Proteins_prot-scriber.out" sort="true" />
+    </test>
+  </tests>
+  <help>
+    <![CDATA[
+
+**What it does**
+    
+prot-scriber_ assigns short human readable descriptions (HRD) to query biological sequences using reference candidate descriptions.
+In this, prot-scriber consumes sequence similarity search (Blast or Diamond or similar) results in tabular format.
+customized lexical analysis is carried out on the descriptions of these Blast Hits and a resulting HRD is assigned to the query sequences.
+For more information, examples and how to use the prot-scriber commandline tool refer to the prot-scriber README_ and MANUAL_.
+
+.. _prot-scriber: http://github.com/usadellab/prot-scriber
+.. _README: https://github.com/usadellab/prot-scriber/blob/master/README.md
+.. _MANUAL: https://github.com/usadellab/prot-scriber/blob/master/README.md#manual
+
+----
+
+**Input**
+
+The input file is one or multiple tabular output(s) of a sequence similarity search (Blast, Diamon or similar).
+Required columns are: 'qacc sacc stitle' (Blast) or 'qseqid sseqid stitle' (Diamond). The input is done via the -s parameter::
+
+    -s, --seq-sim-table
+            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). If the required columns, or more, appear in different order than
+            shown here you must use the --header (-e) argument. If any of the input SSSTs uses a
+            different field-separator than the '<TAB>' character, you must provide the --field-
+            separator (-p) argument. You can provide multiple SSSTs for your query proteins whose information
+            will be combined and evaluated by the tool.
+
+**Input parameters**
+
+prot-scriber gives the user the opportunity to fine tune parameters for the provided input tables.
+To do so turn on the *input configuration* switch. Those are optional, as the tool also provides sensible defaults.
+In case you decide to customize your inputs using below parameters, be advised that prot-scriber expects the
+customized parameter for all input tables - the number of tables and e.g. *--header* parameters have to match.
+You can set the values to 'default' if you want to use the default value for a given input table::
+  
+    -e, --header
+            Header of the --seq-sim-table (-s) arg. Separated by space (' ') the names of the
+            columns in order of appearance in the respective table. Required and default columns are
+            'qacc sacc stitle'. Note that this option only understands Blast terminology, i.e. even
+            if you ran Diamond, please provide 'qacc' instead of 'qseqid' and 'sacc' instead of
+            'sseqid'. Luckily 'stitle' is 'stitle' in Diamond, too. You can have additional columns
+            that will be ignored, as long as the required columns appear in the correct order.
+            Consider this example: 'qacc sacc evalue bitscore stitle'. Set to 'default' to use the hard coded default.
+  
+    -p, --field-separator
+            Field-Separator of the --seq-sim-table (-s) arg. The default value is the '<TAB>' character.
+            Consider this example: ','. You can provide 'default' to use the hard coded default (TAB).
+
+    -b, --blacklist-regexs (Expert option)
+            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. An example file can be downloaded here:
+            https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/blacklist_stitle_regexs.txt.
+
+    -l, --filter-regexs (Expert option)
+            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.
+            Filtering is used to process descriptions ('stitle' in Blast terminology) and prepare
+            the descriptions for the prot-scriber annotation process. In case of UniProt sequence
+            similarity search results (Blast result tables), this removes the Blast Hit identifier
+            (`sacc`) from the description (`stitle`) and also removes the taxonomic information
+            starting with e.g. 'OS=' at the end of the `stitle` strings. Set to 'default' to use 
+            hard coded default. Anexample file can be downloaded here:
+            https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/filter_stitle_regexs.txt.
+
+    -c, --capture-replace-pairs (Expert option)
+            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. This means the second
+            line contains the capture groups. These pairs are used to further filter
+            the sequence similarity search result descriptions ('stitle' in Blast terminology). In
+            contrast to the --filter-regex (-l) matches are not deleted, but replaced with the
+            second line of the pair. Filtering is used to process descriptions ('stitle' in Blast
+            terminology) and prepare the descriptions for the prot-scriber annotation process.
+            Set to 'default' to use the hard coded default. An example file can be downloaded here:
+            https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/capture_replace_pairs.txt.
+
+----
+
+**Gene family annotation**
+
+prot-scriber can also apply the same methodology to produce HRDs for sets of biological sequences, i.e. gene families::
+
+    -f, --seq-families
+            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.
+
+    -g, --seq-family-gene-ids-separator 
+            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+)'.
+
+    -a, --annotate-non-family-queries
+            Use this option only in combination with --seq-families (-f), i.e. when prot-scriber is
+            used to generate human readable descriptions for gene families. If in that context this
+            flag is given, queries for which there are sequence similarity search (Blast) results
+            but that are NOT member of a sequence family will receive an annotation (human readable
+            description) in the output file, too. Default value of this setting is 'OFF' (false).
+
+----
+
+**Expert options**
+
+Some additional optional configuration. Only use when you know what you are doing::
+
+    -w, --non-informative-words-regexs
+            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 minimun
+            score in the prot-scriber process that generates human readable description. There is a
+            default list hard-coded into prot-scriber. An example file can be downloaded here:
+            https://raw.githubusercontent.com/usadellab/prot-scriber/master/misc/non_informative_words_regexs.txt.
+
+    -r, --description-split-regex
+            A regular expression to be used to split descriptions (`stitle` in Blast
+            terminology) into words. Default is '([~_\-/|\;,':.\s]+)'.
+
+    -q, --center-inverse-word-information-content-at-quantile
+            The quantile (percentile) to be subtracted from calculated inverse word information
+            content to center these values. Consequently, this must be a value between zero and one
+            or literal 50, which is interpreted as mean instead of a quantile. Default is 50,
+            implying centering at the mean.
+
+----
+
+**Output**
+
+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::
+
+    Annotee-Identifier	Human-Readable-Description
+    Soltu.DM.02G020600.1	arath strubbelig receptor family
+    Soltu.DM.S001650.1	germin member
+    Soltu.DM.03G011280.1	increased dna methylation
+    ...
+
+    ]]>
+  </help>
+</tool>