--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/recentrifuge.xml	Wed Apr 06 10:31:22 2022 +0000
@@ -0,0 +1,509 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<tool id="recentrifuge" name="Recentrifuge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+  <description>
+    Robust comparative analysis and contamination removal for metagenomics
+  </description>
+  <macros>
+    <import>macro.xml</import>
+  </macros>
+  <expand macro='xrefs'/>
+  <expand macro="requirements" />
+  <expand macro="version_command" />
+  <command detect_errors="aggressive"><![CDATA[
+    ## database input ##
+    ## if database imported from history ##
+    #if $database.db_type.db_select == "cached"
+      #set $rcf_db = $database.db_type.cached_db.fields.path
+    #else if $database.db_type.db_select == "history"
+      mkdir rcf_db &&
+      #for i in $database.db_type.history_db
+        ln -s '$i' 'rcf_db/$i.element_identifier' &&
+      #end for
+      #set $rcf_db = "rcf_db"
+    #end if
+    rcf
+    -n $rcf_db
+    ## input type ##
+    #if $input_option.file_type.filetype == "centrifuge"
+      -f '$input_option.input_file'
+    #else if $input_option.file_type.filetype == "lmat"
+      -l '$input_option.input_file'
+    #else if $input_option.file_type.filetype == "clark"
+      -r '$input_option.input_file'
+    #else if $input_option.file_type.filetype == "kraken"
+      -k '$input_option.input_file'
+    #else if $input_option.file_type.filetype == "generic"
+      -g '$input_option.input_file'
+      --format '$input_option.file_type.format'
+    #end if
+    ## output option ##
+    -e $output_option.extra
+    -o output
+    $output_option.pickle
+    $output_option.nohtml
+    ## advanced options ##
+    #if $advanced_option.control_select.controls_type == "add_neg"
+      --controls '$advanced_option.control_select.controls'
+    #end if
+    #if $advanced_option.scoring != "DEFAULT"
+      --scoring '$advanced_option.scoring'
+    #end if
+    #if $advanced_option.minscore_select.minscore == "specify_minscore"
+      --minscore '$advanced_option.minscore_select.minscore_value'
+    #end if
+    #if $advanced_option.mintaxa_type.mintaxa_select == "specify_mintaxa"
+      --mintaxa '$advanced_option.mintaxa_type.mintaxa'
+    #end if
+    #if $advanced_option.exclude_taxa_type.exclude_taxa_select == "yes_exclude"
+      --exclude '$advanced_option.exclude_taxa_type.exclude_taxa_name'
+    #end if
+    #if $advanced_option.include_taxa_type.include_taxa_select == "yes_include"
+      --include '$advanced_option.include_taxa_type.include_taxa_name'
+    #end if
+    $advanced_option.avoidcross
+    ## MORE ADVANCED OPTION ##
+    #if $more_advanced_option.minscore_type.minscore_select == "specify_minscore"
+      --ctrlminscore '$more_advanced_option.minscore_type.ctrlminscore'
+    #end if
+    #if $more_advanced_option.ctrlmintaxa_type.ctrlmintaxa_select =="specify_ctrlmintaxa"
+      --ctrlmintaxa '$more_advanced_option.ctrlmintaxa_type.ctrlmintaxa'
+    #end if
+    --summary $more_advanced_option.summary
+    $more_advanced_option.takeoutroot
+    $more_advanced_option.nokollapse
+    $more_advanced_option.strain
+    $more_advanced_option.sequential
+    $more_advanced_option.debug
+    $more_advanced_option.version
+    ## LOG FILE OUTPUT ##
+    &> $logfile
+    ]]>
+
+  </command>
+  <inputs>
+    <!-- INPUT FILES -->
+    <section name="input_option" title="Input options" expanded="true">
+      <param name="input_file" type="data" format="tabular" label="Select taxonomy file tabular formated"/>
+      <conditional name="file_type">
+        <param name="filetype" type="select" label="Type of input file (centrifuge, CLARK, Generic, kraken, LMAT)" help="(-f, -r, -g, -k, -l)">
+          <option value="centrifuge">Centrifuge</option>
+          <option value="clark">CLARK</option>
+          <option value="generic">Generic</option>
+          <option value="lmat" >LMAT</option>
+          <option value="kraken" >Kraken</option>
+        </param>
+        <when value="centrifuge"/>
+        <when value="lmat"/>
+        <when value="clark"/>
+        <when value="kraken"/>
+        <when value="generic">
+          <param argument="--format" type="text" label="Format of the output files from a generic classifier"
+                 help="string like 'TYP:csv,TID:1,LEN:3,SCO:6,UNC:0'
+                       where valid file TYPes are csv/tsv/ssv, and the rest of fields indicate the number of column used (starting in 1)
+                       for the TaxIDs assigned,the LENgth of the read, the SCOre given to the assignment (--format)">
+          </param>
+        </when>
+      </conditional>
+    </section>
+    <!-- taxa databases -->
+    <section name="database" title="Database type" expanded="true">
+      <conditional name="db_type">
+        <param name="db_select" type="select" label="Cached database with clade-specific marker genes">
+          <option value="cached" selected="true">Locally installed</option>
+          <option value="history">From history</option>
+        </param>
+        <when value="cached">
+          <param name="cached_db" type="select" label="Cached database whith taxa ID">
+            <options from_data_table="rcf_database">
+              <validator message="No recentrifuge database is available" type="no_options"/>
+            </options>
+          </param>
+        </when>
+        <when value="history">
+          <param name="history_db" type="data" multiple="true" format="txt" label="Database from history"/>
+        </when>
+      </conditional>
+    </section>
+    <!-- output name -->
+    <section name="output_option" title="Output options">
+      <param argument="--extra" type="select" label="Type of extra output to be generated (default on CSV)" help="(--extra)">
+        <option value="CSV" selected="true" >CSV</option>
+        <option value="DYNOMICS">DYNOMICS</option>
+        <option value="FULL">FULL</option>
+        <option value="MULTICSV">MULTICSV</option>
+        <option value="TSV" >TSV</option>
+      </param>
+      <param argument="--pickle" type="boolean" truevalue="--pickle" falsevalue="" label="Serialize statistics and data results in pandas DataFrames" help="(--pickle)"/>
+      <param argument="--nohtml" type="boolean" truevalue="--nohtml" falsevalue="" label="Suppress saving the HTML output file" help="(--nohtml)"/>
+    </section>
+    <!-- ADVANCED OPTIONS -->
+    <section name="advanced_option" title="Coarse tuning of algorithm parameters">
+      <conditional name="control_select">
+        <param name="controls_type" type="select" label="Number of first samples will be treated as negative controls (default is 0)" help="(--controls)">
+          <option value="default">No control</option>
+          <option value="add_neg">Add negative controls </option>
+        </param>
+        <when value="default">
+        </when>
+        <when value="add_neg">
+          <param name="controls" type="integer" min="0" value="0" label="Number of samples"/>
+        </when>
+      </conditional>
+        <param name="scoring" type="select" label="Type of scoring to be applied" help="(--scoring)">
+          <option value="DEFAULT" selected="true">Default scoring</option>
+          <option value="SHEL">SHEL</option>
+          <option value="LENGTH">LENGTH</option>
+          <option value="LOGLENGTH">LOGLENGTH</option>
+          <option value="NORMA">NORMA</option>
+          <option value="LMAT">LMAT</option>
+          <option value="CLARK_C">CLARK_C</option>
+          <option value="CLARK_G">CLARK_G</option>
+          <option value="KRAKEN">KRAKEN</option>
+          <option value="GENERIC">GENERIC</option>
+        </param>
+      <conditional name="minscore_select">
+        <param name="minscore" type="select" label="minimum score/confidence of the classification of a read to pass the quality filter; all pass by default" help="(--minscore)">
+          <option value="default" selected="true">Default all pass</option>
+          <option value="specify_minscore">Specify value</option>
+        </param>
+        <when value="default">
+        </when>
+        <when value="specify_minscore">
+          <param name="minscore_value" type="integer" min="0" value="0" label="minimum score/confidence value"/>
+        </when>
+      </conditional>
+      <conditional name="mintaxa_type">
+        <param name="mintaxa_select" type="select" label="Minimum taxa to avoid collapsing one level into the parent (if not specified a value will be automatically assigned)" help="(--mintaxa)">
+          <option value="default" selected="true">Automatically assigned</option>
+          <option value="specify_mintaxa">Choose value</option>
+        </param>
+        <when value="default">
+        </when>
+        <when value="specify_mintaxa">
+          <param name="mintaxa" type="integer" min="0" value="0" label="Minimum taxa number"/>
+        </when>
+      </conditional>
+      <conditional name="exclude_taxa_type">
+        <param name="exclude_taxa_select" type="select" label="NCBI taxid code to exclude a taxon and all underneath (default, no exclude)" help="(--exclude)">
+          <option value="no_exclude">No exclusion</option>
+          <option value="yes_exclude">Specify excluded taxa</option>
+        </param>
+        <when value="yes_exclude">
+          <param name="exclude_taxa_name" type="text" label="NCBI taxid code to exclude" />
+        </when>
+        <when value="no_exclude"/>
+      </conditional>
+      <conditional name="include_taxa_type">
+        <param name="include_taxa_select" type="select" label="NCBI taxid code to include a taxon and all underneath" help="(--include)">
+          <option value="no_include">Default no taxa include</option>
+            <option value="yes_include">Specify included taxa</option>
+        </param>
+        <when value="yes_include">
+          <param name="include_taxa_name" type="text" label="NCBI taxid code to include"/>
+        </when>
+        <when value="no_include"/>
+        </conditional>
+          <param argument="--avoidcross" type="boolean" truevalue="--avoidcross" falsevalue="" label="Avoid cross analysis" help="(--avoidcross)"> </param>
+    </section>
+    <!-- Detailed more fine parameters -->
+    <section name="more_advanced_option" title=" Fine tuning of algorithm parameters">
+      <conditional name="minscore_type">
+        <param name="minscore_select" type="select" label="minimum score/confidence of the classification of a read in control samples to pass the quality filter; it defaults to minscore" help="(--ctrlminscore)">
+          <option value="default_minscore">Default minscore</option>
+          <option value="specify_minscore">Specify minscore</option>
+        </param>
+        <when value="default_minscore"/>
+        <when value="specify_minscore">
+          <param name="ctrlminscore" type="integer" value="0" label="minimum score/confidence"/>
+        </when>
+      </conditional>
+      <conditional name="ctrlmintaxa_type">
+        <param name="ctrlmintaxa_select" type="select" label="Minimum taxa to avoid collapsing one level into the parent" help="(--ctrlmintaxa)">
+          <option value="default_ctrlmintaxa">Default value</option>
+          <option value="specify_ctrlmintaxa">Specify minimum taxa number</option>
+        </param>
+        <when value="default_ctrlmintaxa"/>
+        <when value="specify_ctrlmintaxa">
+          <param name="ctrlmintaxa"  type="integer" value="0" label="Minimum taxa number"/>
+        </when>
+      </conditional>
+      <param name="summary" type="select" label="select to 'add' summary samples to other samples, or to 'only' show summary samples or to 'avoid' summaries at all" help="(--summary)">
+        <option value="ADD" selected="true">ADD</option>
+        <option value="ONLY">ONLY</option>
+        <option value="AVOID">AVOID</option>
+      </param>
+      <param argument="--takeoutroot" type="boolean" truevalue="--takeoutroot" falsevalue="" label="remove counts directly assigned to the root level" help="(--takeoutroot)"/>
+      <param argument="--nokollapse"  type="boolean" truevalue="--nokollapse" falsevalue=""  label="show the cellular organisms taxon" help="(--nokollapse)"/>
+      <param argument="--strain"      type="boolean" truevalue="--strain" falsevalue=""      label="Strain level instead of species as the resolution limit for the robust contamination removal algorithm; use with caution, this is an experimental feature" help="(--strain)" />
+      <param argument="--sequential"  type="boolean" truevalue="--sequential" falsevalue=""  label="deactivate parallel processing" help="(--sequential)" />
+      <param argument="--debug"       type="boolean" truevalue="--debug" falsevalue=""       label="increase output verbosity and perform additional checks" help="(--debug)" />
+      <param argument="--version"     type="boolean" truevalue="--version" falsevalue=""     label=" show program's version number and exit" help="(--version)" />
+    </section>
+  </inputs>
+  <!-- OUTPUT FILE, TYPE DEPENDING ON extra PARAMETER -->
+  <outputs>
+    <data name="html_report" format="html" from_work_dir="output.rcf.html" label="${tool.name} on ${on_string}: html report">
+      <filter> output_option['nohtml'] == False</filter>
+    </data>
+    <data name="logfile" format="txt" label="${tool.name} on ${on_string}: log file"/>
+
+    <data name="data_csv" format="csv" from_work_dir="output.rcf.data.csv" label="${tool.name} on ${on_string}: data.csv">
+      <filter> output_option['extra']  == 'CSV' </filter>
+    </data>
+    <data name="stat_csv" format="csv" from_work_dir="output.rcf.stat.csv" label="${tool.name} on ${on_string}: stat csv">
+        <filter> output_option['extra'] == 'CSV' or output_option['extra'] == 'MULTICSV' </filter>
+    </data>
+    <data name="data_tsv" format="tabular" from_work_dir="output.rcf.data.tsv" label="${tool.name} on ${on_string}: data tsv">
+        <filter> output_option['extra'] == 'TSV' </filter>
+    </data>
+    <data name="stat_tsv" format="tabular" from_work_dir="output.rcf.stat.tsv" label="${tool.name} on ${on_string}: stat tsv">
+      <filter> output_option['extra'] == 'TSV' </filter>
+    </data>
+    <data name="xls_report" format="xlsx" from_work_dir="output.rcf.xlsx" label="${tool.name} on ${on_string}: xlsx report">
+      <filter> output_option['extra'] == 'FULL' or output_option['extra'] == 'DYNOMICS'</filter>
+    </data>
+    <data name="stat_bz" format="bz2" from_work_dir="output.rcf.stat.pkl.bz2" label="${tool.name} on ${on_string}: stat.pkl.bz2">
+        <filter> output_option['pickle'] == True </filter>
+    </data>
+    <data name="data_bz" format="bz2" from_work_dir="output.rcf.data.pkl.bz2" label="${tool.name} on ${on_string}: data.pkl.bz2">
+      <filter> output_option['pickle'] == True </filter>
+    </data>
+  </outputs>
+  <tests>
+    <test> <!-- kraken input and CSV output TEST_1-->
+      <section name="database">
+        <conditional name="db">
+          <param name="db_selector" value="cached"/>
+          <param name="cached_db" value="test-db-2022"/>
+        </conditional>
+      </section>
+      <section name="input_option">
+        <param name="input_file" value="kraken_test/kraken.out"/>
+        <conditional name="file_type">
+          <param name="filetype" value="kraken"/>
+        </conditional>
+      </section>
+      <section name="output_option">
+        <param name="output_type" value="default_type"/>
+      </section>
+      <section name="more_advanced_option">
+        <param name="summary" value="AVOID"/>
+      </section>
+      <output name="data_csv" file="kraken_test/test1_csv.rcf.data.csv" lines_diff="2"/>
+      <output name="stat_csv" file="kraken_test/test1_csv.rcf.stat.csv" lines_diff="2"/>
+      <output name="html_report" file="kraken_test/test1_csv.rcf.html" lines_diff="2"/>
+      <output name="logfile" file="kraken_test/test1_csv.log" lines_diff="7"/>
+    </test>
+    <test> <!-- centrifuge input and full options with imported database TEST_2 -->
+      <section name="database">
+        <conditional name="db">
+          <param name="db_selector" value="history"/>
+          <param name="history_db" value="test-db/delnodes.dmp,test-db/division.dmp,test-db/gc.prt,test-db/gencode.dmp,test-db/merged.dmp,test-db/names.dmp,test-db/nodes.dmp,test-db/readme.txt"/>
+        </conditional>
+      </section>
+      <section name="input_option">
+        <param name="input_file" value="centrifuge_test/centrifuge.out"/>
+        <conditional name="file_type">
+          <param name="filetype" value="centrifuge"/>
+        </conditional>
+      </section>
+      <section name="output_option">
+        <param name="extra" value="MULTICSV"/>
+        <param name="pickle" value="false"/>
+        <param name="nohtml" value="true"/>
+      </section>
+      <section name="advanced_option">
+        <conditional name="control_select">
+          <param name="controls_type"  value="add_neg"/>
+          <param name="controls" value="0"/>
+        </conditional>
+        <param name="scoring" value="NORMA"/>
+        <conditional name="minscore_select">
+          <param name="minscore" value="specify_minscore"/>
+          <param name="minscore_value" value="0"/>
+        </conditional>
+        <param name="avoidcross" value="true"/>
+      </section>
+      <section name="more_advanced_option">
+        <conditional name="minscore_type">
+          <param name="minscore_select" value="specify_minscore"/>
+          <param name="ctrlminscore" value="0"/>
+        </conditional>
+        <param name="summary" value="AVOID"/>
+      </section>
+      <output name="stat_csv" file="centrifuge_test/test2_multicsv.rcf.stat.csv" lines_diff="2"/>
+      <output name="logfile" file="centrifuge_test/test2_multicsv.log" lines_diff="20"/>
+    </test>
+    <test> <!-- kraken input cached DB several option added and .bz2 files generated TEST_3 -->
+      <section name="database">
+        <conditional name="db_type">
+          <param name="db_select" value="cached"/>
+          <param name="cached_db" value="test-db-2022"/>
+        </conditional>
+      </section>
+        <section name="input_option">
+          <param name="input_file" value="kraken_test/kraken.out"/>
+          <conditional name="file_type">
+            <param name="filetype" value="kraken"/>
+          </conditional>
+        </section>
+          <section name="output_option" >
+            <param name="extra" value="TSV"/>
+            <param name="pickle" value="false"/>
+            <param name="nohtml" value="true"/>
+          </section>
+        <section name="advanced_option">
+          <param name="scoring" value="LOGLENGTH"/>
+        </section>
+        <section name="more_advanced_option">
+          <param name="summary" value="ONLY"/>
+          <param name="strain" value="true"/>
+        </section>
+      <output name="data_tsv" file="kraken_test/test3_rcf.data.tsv" lines_diff="2"/>
+      <output name="stat_tsv" file="kraken_test/test3_rcf.stat.tsv" lines_diff="2"/>
+      <output name="logfile" file="kraken_test/test3_tsv.log" lines_diff="20"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+    =-= /home/pierre/anaconda3/envs/rcf/bin/rcf =-= v1.8.1 - Mar 2022 =-= by Jose Manuel Martí =-=
+
+  usage: rcf [-h] [-V] [-n PATH] [--format GENERIC_FORMAT]
+             (-f FILE | -g FILE | -l FILE | -r FILE | -k FILE) [-o FILE]
+             [-e OUTPUT_TYPE] [-p] [--nohtml] [-a | -c CONTROLS_NUMBER]
+             [-s SCORING] [-y NUMBER] [-m INT] [-x TAXID] [-i TAXID] [-z NUMBER]
+             [-w INT] [-u SUMMARY_BEHAVIOR] [-t] [--nokollapse] [-d] [--strain]
+             [--sequential]
+
+  Robust comparative analysis and contamination removal for metagenomics
+
+  options:
+    -h, --help            show this help message and exit
+    -V, --version         show program's version number and exit
+
+  input:
+    Define Recentrifuge input files and formats
+
+    -n PATH, --nodespath PATH
+                          path for the nodes information files (nodes.dmp and
+                          names.dmp from NCBI)
+    --format GENERIC_FORMAT
+                          format of the output files from a generic classifier
+                          included with the option -g; It is a string like
+                          "TYP:csv,TID:1,LEN:3,SCO:6,UNC:0" where valid file
+                          TYPes are csv/tsv/ssv, and the rest of fields indicate
+                          the number of column used (starting in 1) for the
+                          TaxIDs assigned, the LENgth of the read, the SCOre
+                          given to the assignment, and the taxid code used for
+                          UNClassified reads
+    -f FILE, --file FILE  Centrifuge output files; if a single directory is
+                          entered, every .out file inside will be taken as a
+                          different sample; multiple -f is available to include
+                          several Centrifuge samples
+    -g FILE, --generic FILE
+                          output file from a generic classifier; it requires the
+                          flag --format (see such option for details); multiple
+                          -g is available to include several generic samples
+    -l FILE, --lmat FILE  LMAT output dir or file prefix; if just "." is
+                          entered, every subdirectory under the current
+                          directory will be taken as a sample and scanned
+                          looking for LMAT output files; multiple -l is
+                          available to include several samples
+    -r FILE, --clark FILE
+                          CLARK full-mode output files; if a single directory is
+                          entered, every .csv file inside will be taken as a
+                          different sample; multiple -r is available to include
+                          several CLARK, CLARK-l, and CLARK-S full-mode samples
+    -k FILE, --kraken FILE
+                          Kraken output files; if a single directory is entered,
+                          every .krk file inside will be taken as a different
+                          sample; multiple -k is available to include several
+                          Kraken (version 1 or 2) samples
+
+  output:
+    Related to the Recentrifuge output files
+
+    -o FILE, --outprefix FILE
+                          output prefix; if not given, it will be inferred from
+                          input files; an HTML filename is still accepted for
+                          backwards compatibility with legacy --outhtml option
+    -e OUTPUT_TYPE, --extra OUTPUT_TYPE
+                          type of extra output to be generated, and can be one
+                          of ['FULL', 'CSV', 'MULTICSV', 'TSV', 'DYNOMICS']
+    -p, --pickle          pickle (serialize) statistics and data results in
+                          pandas DataFrames (format affected by selection of
+                          --extra)
+    --nohtml              suppress saving the HTML output file
+
+  tuning:
+    Coarse tuning of algorithm parameters
+
+    -a, --avoidcross      avoid cross analysis
+    -c CONTROLS_NUMBER, --controls CONTROLS_NUMBER
+                          this number of first samples will be treated as
+                          negative controls; default is no controls
+    -s SCORING, --scoring SCORING
+                          type of scoring to be applied, and can be one of
+                          ['SHEL', 'LENGTH', 'LOGLENGTH', 'NORMA', 'LMAT',
+                          'CLARK_C', 'CLARK_G', 'KRAKEN', 'GENERIC']
+    -y NUMBER, --minscore NUMBER
+                          minimum score/confidence of the classification of a
+                          read to pass the quality filter; all pass by default
+    -m INT, --mintaxa INT
+                          minimum taxa to avoid collapsing one level into the
+                          parent (if not specified a value will be automatically
+                          assigned)
+    -x TAXID, --exclude TAXID
+                          NCBI taxid code to exclude a taxon and all underneath
+                          (multiple -x is available to exclude several taxid)
+    -i TAXID, --include TAXID
+                          NCBI taxid code to include a taxon and all underneath
+                          (multiple -i is available to include several taxid);
+                          by default, all the taxa are considered for inclusion
+
+  fine tuning:
+    Fine tuning of algorithm parameters
+
+    -z NUMBER, --ctrlminscore NUMBER
+                          minimum score/confidence of the classification of a
+                          read in control samples to pass the quality filter; it
+                          defaults to "minscore"
+    -w INT, --ctrlmintaxa INT
+                          minimum taxa to avoid collapsing one level into the
+                          parent (if not specified a value will be automatically
+                          assigned)
+    -u SUMMARY_BEHAVIOR, --summary SUMMARY_BEHAVIOR
+                          choice for summary behaviour, and can be one of
+                          ['ADD', 'ONLY', 'AVOID']
+    -t, --takeoutroot     remove counts directly assigned to the "root" level
+    --nokollapse          show the "cellular organisms" taxon
+
+  advanced:
+    Advanced modes of running
+
+    -d, --debug           increase output verbosity and perform additional
+                          checks
+    --strain              set strain level instead of species as the resolution
+                          limit for the robust contamination removal algorithm;
+                          use with caution, this is an experimental feature
+    --sequential          deactivate parallel processing
+
+  rcf - Release 1.8.1 - Mar 2022
+
+      Copyright (C) 2017–2022, Jose Manuel Martí Martínez
+
+      This program is free software: you can redistribute it and/or modify
+      it under the terms of the GNU Affero General Public License as
+      published by the Free Software Foundation, either version 3 of the
+      License, or (at your option) any later version.
+
+      This program is distributed in the hope that it will be useful,
+      but WITHOUT ANY WARRANTY; without even the implied warranty of
+      MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+      GNU Affero General Public License for more details.
+
+      You should have received a copy of the GNU Affero General Public License
+      along with this program.  If not, see <https://www.gnu.org/licenses/>.
+    ]]></help>
+    <expand macro="citations"/>
+    </tool>