--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Tue Dec 10 16:05:34 2019 -0500
@@ -0,0 +1,389 @@
+<macros>
+    <token name="@VERSION@">5.0.3</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">cat</requirement>
+            <yield/>
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[CAT --version]]></version_command>
+    </xml>
+    <token name="@DATABASE_FOLDER@">CAT_database</token>
+    <token name="@TAXONOMY_FOLDER@">taxonomy</token>
+    <xml name="cat_db">
+        <conditional name="db">
+            <param name="db_src" type="select" label="CAT database (--database_folder,--taxonomy_folder) from">
+                <option value="cached">local cached database</option>
+                <option value="history">history</option>
+            </param>
+            <when value="cached">
+                <param name="cat_builtin" type="select" label="Use a built-in CAT database" help="If the CAT database of interest is not listed, contact your Galaxy administrator">
+                    <options from_data_table="cat_database">
+                        <filter type="sort_by" column="2" />
+                        <validator type="no_options" message="No CAT database is available." />
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="cat_db" type="data" format="txt" label="A history dataset from CAT prepare tool"/>
+            </when>
+        </conditional>
+    </xml>
+    <token name="@CAT_DB@"><![CDATA[
+        #if $db.db_src == 'cached':
+        --database_folder '$db.cat_builtin.fields.database_folder'
+        --taxonomy_folder '$db.cat_builtin.fields.taxonomy_folder'
+        #else
+        #import os.path
+        #set $catdb = $db.cat_db.extra_files_path
+        --database_folder '$os.path.join($catdb,"@DATABASE_FOLDER@")'
+        --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")'
+        #end if
+]]></token>
+    <token name="@CAT_TAXONOMY@"><![CDATA[
+        #if $db.db_src == 'cached':
+        --taxonomy_folder '$db.cat_builtin.fields.taxonomy_folder'
+        #else
+        #import os.path
+        #set $catdb = $db.cat_db.extra_files_path
+        --taxonomy_folder '$os.path.join($catdb,"@TAXONOMY_FOLDER@")'
+        #end if
+]]></token>
+    <xml name="test_catdb">
+        <conditional name="db">
+            <param name="db_src" value="cached"/>
+            <param name="cat_builtin" value="CAT_prepare_test"/>
+        </conditional>
+    </xml>
+    <xml name="use_intermediates">
+        <conditional name="previous">
+            <param name="use_previous" type="select" label="Use previous prodigal gene prediction and diamond alignment">
+                <help>predicted_proteins.faa and alignment.diamond from previous CAT run.</help> 
+                <option value="yes">Yes</option>
+                <option value="no" selected="true">No</option>
+            </param>
+            <when value="yes">
+                <param argument="--proteins_fasta" type="data" format="fasta" label="prodigal predicted proteins fasta"/>
+                <param argument="--diamond_alignment" type="data" format="tabular" label="alignment.diamond file"/>
+            </when>
+            <when value="no"/>
+        </conditional>
+    </xml>
+    <token name="@USE_INTERMEDIATES@"><![CDATA[
+      #if $previous.use_previous == 'yes'
+      --proteins_fasta '$previous.proteins_fasta'
+      --diamond_alignment '$previous.diamond_alignment'
+      #end if
+      --out_prefix 'cat_output'
+]]></token>
+    <xml name="custom_settings">
+        <param argument="--range" type="integer" value="10" min="0" max="49" label="range"/>
+        <param argument="--fraction" type="float" value="0.5" min="0" max="0.99" label="fraction"/>
+    </xml>
+    <token name="@CUSTOM_SETTINGS@"><![CDATA[
+      --range '$range'
+      --fraction '$fraction'
+]]></token>
+    <xml name="diamond_options">
+        <conditional name="diamond">
+            <param name="set_diamond_opts" type="select" label="Set advanced diamond options">
+                <option value="yes">Yes</option>
+                <option value="no" selected="true">No</option>
+            </param>
+            <when value="yes">
+                <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false" 
+                    label="Run DIAMOND in sensitive mode (considerably slower)"/>
+                <param argument="--block_size" type="float" value="2.0" min="1" max="10" label="DIAMOND block-size parameter."
+                    help="lower will decrease memory and temporary disk space usage, higher will increase performance."/>
+                <param argument="--index_chunks" type="integer" value="4" min="1" max="10" label="DIAMOND index-chunks parameter" 
+                    help="Set to 1 on high memory machines. The parameter has no effect on temporary disk space usage."/>
+                <param argument="--top" type="integer" value="50" min="1" max="50" label="DIAMOND top parameter" 
+                    help="Governs hits within range of best hit that are written to the alignment file. This implies you know what you are doing."/>
+            </when>
+            <when value="no"/>
+        </conditional>
+    </xml>
+    <token name="@DIAMOND_OPTIONS@"><![CDATA[
+        #if $diamond.set_diamond_opts == 'yes':
+            $diamond.sensitive
+            --block_size '$diamond.block_size'
+            --index_chunks '$diamond.index_chunks'
+            #if $diamond.top < 50:
+                --I_know_what_Im_doing
+                --top '$diamond.top'
+            #end if
+        #end if
+]]></token>
+
+    <xml name="add_names_options">
+        <param argument="--only_official" type="boolean" truevalue="--only_official" falsevalue="" checked="true" 
+            label="Only output official level names."/>
+        <param argument="--exclude_scores" type="boolean" truevalue="--exclude_scores" falsevalue="" checked="false" 
+            label="Exclude bit-score support scores in the lineage."/>
+    </xml>
+    <token name="@ADD_NAMES_OPTIONS@"><![CDATA[
+    $only_official $exclude_scores 
+]]></token>
+    <xml name="add_names">
+        <conditional name="names">
+            <param name="add_names" type="select" label="CAT add_names for" 
+                help="annotate with taxonomic names."> 
+                <option value="no">No</option>
+                <option value="orf2lca">ORF2LCA.names.txt</option>
+                <option value="classification">classification.names.txt</option>
+                <option value="both">ORF2LCA.names.txt and classification.names.txt</option>
+            </param>
+            <when value="no"/>
+            <when value="orf2lca">
+                <expand macro="add_names_options"/>
+            </when>
+            <when value="classification">
+                <expand macro="add_names_options"/>
+            </when>
+            <when value="both">
+                <expand macro="add_names_options"/>
+            </when>
+        </conditional>
+    </xml>
+    <token name="@TXT2TSV@">${__tool_directory__}/tabpad.py</token>
+    <token name="@ADD_NAMES@"><![CDATA[
+    #if $names.add_names in ['classification','both']:
+        && CAT add_names $names.only_official $names.exclude_scores 
+            @CAT_TAXONOMY@
+            #if $bcat == 'CAT'
+                -i 'cat_output.contig2classification.tsv'
+            #else
+                -i 'cat_output.bin2classification.tsv'
+            #end if
+            -o 'classification_names.txt'
+        && ${__tool_directory__}/tabpad.py -i 'classification_names.txt' -o '$classification_names'
+    #end if
+    #if $names.add_names in ['orf2lca','both']:
+        && CAT add_names $names.only_official $names.exclude_scores 
+            @CAT_TAXONOMY@
+            -i 'cat_output.ORF2LCA.tsv'
+            -o 'orf2lca_names.txt'
+        && ${__tool_directory__}/tabpad.py -i 'orf2lca_names.txt' -o '$orf2lca_names'
+    #end if
+]]></token>
+    <xml name="summarise">
+        <param name="summarise" type="select" label="CAT summarise report" 
+            help="Report the number of assignments to each taxonomic name">
+            <option value="no">No</option>
+            <option value="classification">classification.summary.txt</option>
+        </param>
+    </xml>
+    <token name="@SUMMARISE@"><![CDATA[
+    #if $summarise in ['classification']:
+        #if $names.add_names in ['classification','both'] and $names.only_official: 
+            #set $summary_input = $classification_names
+        #else 
+            #set $summary_input = 'classification_offical_names'
+            && CAT add_names --only_official
+                @CAT_TAXONOMY@
+                #if $bcat == 'CAT'
+                    -i 'cat_output.contig2classification.tsv'
+                #else
+                    -i 'cat_output.bin2classification.tsv'
+                #end if
+                -o '$summary_input'
+        #end if
+        && CAT summarise 
+            #if $bcat == 'CAT'
+                -c '$contigs_fasta'
+            #end if
+            -i '$summary_input'
+            -o 'classification_summary.txt'
+        && ${__tool_directory__}/tabpad.py -i 'classification_summary.txt' -o '$classification_summary'
+    #end if
+]]></token>
+    
+    <xml name="select_outputs">
+        <param name="select_outputs" type="select" multiple="true" optional="false" label="Select outputs">
+            <option value="log" selected="true">log</option>
+            <option value="predicted_proteins_faa" selected="true">Prodigal predicted_proteins.faa</option>
+            <option value="predicted_proteins_gff">Prodigal predicted_proteins.gff</option>
+            <option value="alignment_diamond">Diamond blastp alignment.diamond</option>
+            <option value="orf2lca" selected="true">ORF2LCA.txt (taxonomic assignment per predicted ORF)</option>
+            <yield/>
+        </param>
+    </xml>
+    <xml name="select_cat_outputs">
+        <param name="bcat" type="hidden" value="CAT"/>
+        <param name="seqtype" type="hidden" value="contig"/>
+        <param name="sum_titles" type="hidden" value="contigs,number of ORFs,number of positions"/>
+        <param name="bin_col" type="hidden" value=""/>
+        <expand macro="select_outputs">
+            <option value="contig2classification" selected="true">contig2classification.txt (taxonomic assignment per contig)</option>
+        </expand>
+    </xml>
+    <xml name="select_bat_outputs">
+        <param name="bcat" type="hidden" value="BAT"/>
+        <param name="seqtype" type="hidden" value="bin"/>
+        <param name="sum_titles" type="hidden" value="bins"/>
+        <param name="bin_col" type="hidden" value="bin,"/>
+        <expand macro="select_outputs">
+            <option value="bin2classification" selected="true">bin2classification.txt (taxonomic assignment per metagenome assembly)</option>
+        </expand>
+    </xml>
+    <xml name="outputs">
+        <data name="log" format="txt" label="${bcat}.log" from_work_dir="cat_output.log">
+            <filter>'log' in select_outputs or not select_outputs</filter>
+        </data>
+        <data name="predicted_proteins_faa" format="fasta" label="${bcat}.predicted_proteins.faa" from_work_dir="cat_output.predicted_proteins.faa">
+            <filter>'predicted_proteins_faa' in select_outputs and previous['use_previous'] == 'no'</filter>
+        </data>
+        <data name="predicted_proteins_gff" format="gff" label="${bcat}.predicted_proteins.gff" from_work_dir="cat_output.predicted_proteins.gff">
+            <filter>'predicted_proteins_gff' in select_outputs and previous['use_previous'] == 'no'</filter>
+        </data>
+        <data name="alignment_diamond" format="tabular" label="${bcat}.alignment.diamond" from_work_dir="cat_output.alignment.diamond">
+            <filter>'alignment_diamond' in select_outputs and previous['use_previous'] == 'no'</filter>
+            <actions>
+                <action name="comment_lines" type="metadata" default="1" />
+                <action name="column_names" type="metadata" default="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore" />
+            </actions>
+        </data>
+        <data name="orf2lca" format="tabular" label="${bcat}.ORF2LCA.txt" from_work_dir="cat_output.ORF2LCA.tsv">
+            <filter>'orf2lca' in select_outputs</filter>
+            <actions>
+                <action name="comment_lines" type="metadata" default="1" />
+                <action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score" />
+            </actions>
+        </data>
+        <data name="contig2classification" format="tabular" label="${bcat}.contig2classification.txt" from_work_dir="cat_output.contig2classification.tsv">
+            <filter>'contig2classification' in select_outputs</filter>
+            <actions>
+                <action name="comment_lines" type="metadata" default="1" />
+                <action name="column_names" type="metadata" default="contig,classification,reason,lineage,lineage scores" />
+            </actions>
+        </data>
+        <data name="bin2classification" format="tabular" label="${bcat}.bin2classification.txt" from_work_dir="cat_output.bin2classification.tsv">
+            <filter>'bin2classification' in select_outputs</filter>
+            <actions>
+                <action name="comment_lines" type="metadata" default="1" />
+                <action name="column_names" type="metadata" default="bin,classification,reason,lineage,lineage scores" />
+            </actions>
+        </data>
+        <data name="orf2lca_names" format="tabular" label="${bcat}.ORF2LCA.names.txt">
+            <filter>names['add_names'] in ['both','orf2lca']</filter>
+            <actions>
+                <action name="comment_lines" type="metadata" default="1" />
+                <action name="column_names" type="metadata" default="ORF,${bin_col}lineage,bit-score,superkingdom,phylum,class,order,family,genus,species" />
+            </actions>
+        </data>
+        <data name="classification_names" format="tabular" label="${bcat}.${seqtype}2classification.names.txt">
+            <filter>names['add_names'] in ['both','classification']</filter>
+            <actions>
+                <action name="comment_lines" type="metadata" default="1" />
+                <action name="column_names" type="metadata" default="${seqtype},classification,reason,lineage,lineage scores,superkingdom,phylum,class,order,family,genus,species" />
+            </actions>
+        </data>
+        <data name="classification_summary" format="tabular" label="${bcat}.${seqtype}2classification.summary.txt">
+            <filter>'classification' in summarise</filter>
+            <actions>
+                <action name="comment_lines" type="metadata" default="4" />
+                <action name="column_names" type="metadata" default="rank,clade,number of ${sum_titles}" />
+            </actions>
+        </data>
+    </xml>
+    <token name="@COMMON_HELP@"><![CDATA[
+The Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) workflows are described at: https://github.com/dutilh/CAT
+
+  - CAT contigs/CAT bins - runs Prodigal_ prokaryotic protein prediction on the fasta input. 
+  - CAT contigs/CAT bins - runs Diamond_ to align predicted proteins to the reference proteins in the CAT database.
+  - CAT contigs/CAT bins - assigns taxonomic classification to fasta entries and ORFs based on alignments. 
+  - CAT add_names - annotates outputs with taxonomic names. 
+  - CAT summerise - reports number of assignments to each taxonomic name.
+
+A CAT database can either be installed by data_manager_cat or in the local history by CAT prepare tool.
+
+.. _Prodigal: https://github.com/hyattpd/Prodigal
+.. _Diamond: https://github.com/bbuchfink/diamond
+
+]]></token>
+    <token name="@OUTPUTS_HELP@"><![CDATA[
+
+**OUTPUTS**
+
+Any of the files produced by the CAT workflow are available as outputs
+  - Prodigal
+
+    - predicted_proteins.faa
+    - predicted_proteins.gff
+
+  - Diamond
+
+    - alignment.diamond
+
+  - CAT contigs/bins
+
+    - contigs/bin2classification.txt
+    - ORF2LCA.txt
+
+  - CAT add_names (optional)
+
+    - contigs/bin2classification.names.txt
+    - ORF2LCA.names.txt
+
+  - CAT summarise (optional)
+
+    - contigs/bin2classification.summary.txt
+
+
+]]></token>
+ 
+    <token name="@OPTIONS_HELP@"><![CDATA[
+
+Optional arguments:
+  -r, --range               cut-off range after alignment [0-49] (default: 10).
+  -f, --fraction            fraction of bit-score support for each classification
+                            [0-0.99] (default: 0.5).
+  -p, --proteins_fasta
+                            Path to predicted proteins fasta file. If supplied,
+                            CAT will skip the protein prediction step.
+  -a, --diamond_alignment
+                            Path to DIAMOND alignment table. If supplied, CAT will
+                            skip the DIAMOND alignment step and directly classify
+                            the sequences. A predicted proteins fasta file should
+                            also be supplied with argument [-p / --proteins].
+
+
+DIAMOND specific optional arguments:
+  --sensitive     Run DIAMOND in sensitive mode (default: not enabled).
+
+  --block_size    DIAMOND block-size parameter (default: 2.0). Lower
+                  numbers will decrease memory and temporary disk space
+                  usage.
+
+  --index_chunks
+                  DIAMOND index-chunks parameter (default: 4). Set to 1
+                  on high memory machines. The parameter has no effect
+                  on temporary disk space usage.
+
+  --top
+                  DIAMOND top parameter [0-50] (default: 50). Governs
+                  hits within range of best hit that are written to the
+                  alignment file. This is not the [-r / --range]
+                  parameter!
+
+
+Setting the DIAMOND --top parameter
+
+You can speed up DIAMOND considerably, and at the same time greatly reduce disk usage, by setting the DIAMOND --top parameter to lower values. This will govern hits within range of the best hit that are written to the alignment file.
+
+You have to be very carefull to 1) not confuse this parameter with the r / --range parameter, which does a similar cut-off but after alignment and 2) be aware that if you want to run CAT or BAT again afterwards with different values of the -r / --range parameter, your options will be limited to the range you have chosen with --top earlier, because all hits that fall outside this range will not be included in the alignment file. Importantly, CAT and BAT currently do not warn you if you choose -r / --range in a second run higher than --top in a previous one, so it's up to you to remember this!
+
+If you have understood all this, or you do not plan to tune -r / --range at all afterwards, you can enjoy a huge speedup with much smaller alignment files! For CAT you can for example set --top 11 and for BAT --top 6.
+
+]]></token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">https://doi.org/10.1101/072868</citation>
+            <citation type="doi">https://doi.org/10.1186/s13059-019-1817-x</citation>
+            <citation type="doi">https://doi.org/10.1038/nmeth.3176</citation>
+            <citation type="doi">https://doi.org/10.1186/1471-2105-11-119</citation>
+            <yield />
+        </citations>
+    </xml>
+</macros>