plast_macros.xml

<macros>
    <xml name="stdio">
        <stdio>
            <!-- Anything other than zero is an error -->
            <exit_code range="1:" />
            <!-- Might see negative return codes for Unix signals via Python subprocess -->
            <exit_code range=":-1" />
            <!-- In case the return code has not been set properly check stderr too -->
            <regex match="Error:" />
            <regex match="Exception:" />
        </stdio>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="binary">@BINARY@</requirement>
            <requirement type="package" version="2.3.0">plast</requirement>
        </requirements>
        <version_command>@BINARY@ -h</version_command>
    </xml>
    <xml name="input_conditional_nucleotide_db">
        <conditional name="db_opts">
            <param name="db_opts_selector" type="select" label="Subject database/sequences">
              <option value="db" selected="True">Locally installed BLAST database</option>
              <option value="histdb">BLAST database from your history</option>
              <option value="file">FASTA file from your history (see warning note below)</option>
            </param>
            <when value="db">
                <param name="database" type="select" label="Nucleotide BLAST database">
                    <options from_file="blastdb.loc">
                      <column name="value" index="0"/>
                      <column name="name" index="1"/>
                      <column name="path" index="2"/>
                    </options>
                </param>
                <param name="histdb" type="hidden" value="" />
                <param name="subject" type="hidden" value="" /> 
            </when>
            <when value="histdb">
                <param name="database" type="hidden" value="" />
                <param name="histdb" type="data" format="blastdbn" label="Nucleotide BLAST database" />
                <param name="subject" type="hidden" value="" />
            </when>
            <when value="file">
                <param name="database" type="hidden" value="" />
                <param name="histdb" type="hidden" value="" />
                <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> 
            </when>
        </conditional>
    </xml>
    <xml name="input_conditional_protein_db">
        <conditional name="db_opts">
            <param name="db_opts_selector" type="select" label="Subject database/sequences">
              <option value="db" selected="True">Locally installed BLAST database</option>
              <option value="histdb">BLAST database from your history</option>
              <option value="file">FASTA file from your history (see warning note below)</option>
            </param>
            <when value="db">
                <param name="database" type="select" label="Protein BLAST database">
                    <options from_file="blastdb_p.loc">
                      <column name="value" index="0"/>
                      <column name="name" index="1"/>
                      <column name="path" index="2"/>
                    </options>
                </param>
                <param name="histdb" type="hidden" value="" />
                <param name="subject" type="hidden" value="" />
            </when>
            <when value="histdb">
                <param name="database" type="hidden" value="" />
                <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database" />
                <param name="subject" type="hidden" value="" />
            </when>
            <when value="file">
                <param name="database" type="hidden" value="" />
                <param name="histdb" type="hidden" value="" />
                <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> 
            </when>
        </conditional>
    </xml>
    <xml name="input_evalue">
        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="E-value threshold" help="Every sequence alignment created by Plast having an E-value less than this threshold will be returned" />
    </xml>
    <xml name="input_max_hits_query">
        <param name="max_hits_query" type="integer" value="0" label="Maximum Hits / Query" help="Maximum number of hits created by Plast for each query. Use zero for default limits (500)">
            <validator type="in_range" min="0" />
        </param>        
    </xml>
    <xml name="input_max_hsp_hits">
        <param name="max_hsp_hits" type="integer" value="0" label="Maximum Hsp / Hits" help="Maximum number of HSPs created by Plast for each hit. Use zero for default limits (HSPs not filtered)">
            <validator type="in_range" min="0" />
        </param>        
    </xml>

    <!-- Extended parameters -->
    <xml name="input_filter_query_default_false">
        <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-F T" falsevalue="-F F" checked="false" />
    </xml>
    <xml name="input_filter_query_default_true">
        <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-F T" falsevalue="-F F" checked="true" />
    </xml>
    <xml name="input_scoring_matrix">
        <param name="matrix" type="select" label="Scoring matrix" help="Similarity matrix used by Plast to compare the two databanks">
            <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
            <option value="BLOSUM50">BLOSUM50</option> 
        </param>
    </xml>
    <xml name="input_gap_costs">
        <param name="gap_costs" type="select" label="Gap costs" help="Penalty costs used by Plast to create and extend gapped sequence alignments">
            <option value="-G 11 -E 2" selected="true">Open:11 Ext:2 (default)</option>
            <option value="-G 9 -E 2" >Open:9 Ext:2</option>
            <option value="-G 8 -E 2" >Open:8 Ext:2</option>
            <option value="-G 7 -E 2" >Open:7 Ext:2</option>
            <option value="-G 6 -E 2" >Open:6 Ext:2</option>
            <option value="-G 12 -E 1" >Open:12 Ext:1</option>
            <option value="-G 11 -E 1" >Open:11 Ext:1</option>
            <option value="-G 10 -E 1" >Open:10 Ext:1</option>
            <option value="-G 9 -E 1" >Open:9 Ext:1</option>
        </param>
    </xml>
    <xml name="input_strand">
        <param name="strand" type="select" label="Query strand(s)" help="Query strand(s) to search against database/subject">
            <option value="-strand both" selected="true">Both (default)</option>
            <option value="-strand plus">Plus (forward)</option>
            <option value="-strand minus">Minus (reverse complement)</option>
        </param>
    </xml>
    <xml name="input_match_mismatch">
        <param name="match_mismatch" type="select" label="Match/Mismatch" help="Reward and penalty for matching and mismatching bases">
            <option value="-r 1 -q -1" >Match:1 Mismatch:-1 </option>
            <option value="-r 1 -q -2" >Match:1 Mismatch:-2 </option>
            <option value="-r 1 -q -3" >Match:1 Mismatch:-3 </option>
            <option value="-r 1 -q -4" >Match:1 Mismatch:-4 </option>
            <option value="-r 2 -q -3" selected="true" >Match:2 Mismatch:-3 (default)</option>
            <option value="-r 4 -q -5" >Match:4 Mismatch:-5 </option>
        </param>
    </xml>
    <xml name="extended_parameters">
        <conditional name="ext_param">
            <param name="ext_param_selector" type="select" label="Extended parameters">
              <option value="basic" selected="True">Hide Extended parameters</option>
              <option value="extended">Show Extended parameters</option>
            </param>
            <when value="basic" />
            <when value="extended">
                <yield />
            </when>
        </conditional>
    </xml>

    <!-- Configuration parameters -->
    <xml name="configuration_parameters">
        <conditional name="config_param">
            <param name="config_param_selector" type="select" label="Algorithm configuration parameters">
              <option value="basic" selected="True">Hide configuration parameters</option>
              <option value="advanced">Show configuration parameters</option>
            </param>
            <when value="basic" />
            <when value="advanced">
                <yield />
            </when>
        </conditional>
    </xml>
    <xml name="input_nb_threads">
        <param name="nb_threads" type="integer" value="8" label="Number of Threads" help="Number of core/threads to execute the Plast command">
            <validator type="in_range" min="0" />
        </param>        
    </xml>
    <xml name="input_max_db_size">
        <param name="max_db_size" type="select" label="Maximum database size" help="Maximum allowed size (in bytes) for a database. If greater, the database is segmented.">
            <option value="20000000" selected="true">20MB (default)</option>
            <option value="50000000">50MB</option>
            <option value="100000000">100MB</option>  
        </param>
    </xml>
    <xml name="input_percent_seed">
        <param name="percent_seed" type="integer" value="1" label="Percent of seeds to use" help="Specify the amount of seeds used by Plast to scan a database. Default is 100%, meaning that Plast will use all seeds to scan the database. Using smaller value may produce similar results while reducing significantly search time">
            <validator type="in_range" min="0" />
        </param>        
    </xml>
    <xml name="input_ungap_threshold_prot">
        <param name="ungap_threshold_prot" type="integer" value="38" label="Ungap threshold" help="Threshold used to computing score to filter the ungap alignments. Default value is 38 for proteins">
            <validator type="in_range" min="0" />
        </param>        
    </xml>
    <xml name="input_ungap_threshold_nucl">
        <param name="ungap_threshold_nucl" type="integer" value="0" label="Ungap threshold" help="Threshold used to computing score to filter the ungap alignments. Default value for nucleotides depends of the E-value (1000>evalue>1e-10 => 35, 1e-10>evalue>1e-30 => 40 ,1e-30>evalue => 45). Zero invoked this default behavior">
            <validator type="in_range" min="0" />
        </param>        
    </xml>
    <xml name="input_ungap_neighboors">
        <param name="ungap_neighboors" type="integer" value="22" label="Ungap neighborhood" help="Set the seed neighborhoods size used to computed left and right score. Default value is 22">
            <validator type="in_range" min="0" />
        </param>        
    </xml>
    <xml name="input_smallgap_threshold">
        <param name="smallgap_threshold" type="integer" value="54" label="Small gap threshold" help="Threshold used to computing score to filter alignments during the small gap algorithm. Default value is 54">
            <validator type="in_range" min="0" />
        </param>        
    </xml>
    <xml name="input_smallgap_bandwidth">
        <param name="smallgap_bandwidth" type="integer" value="16" label="Small gap bandwidth" help="Set the bandwidth size used during the small gap algorithm. Default value is 16">
            <validator type="in_range" min="0" />
        </param>        
    </xml>
    <xml name="input_ungap_Xdrop">
        <param name="ungap_Xdrop" type="integer" value="20" label="Ungap Xdrop" help="Xdrop value used to filter alignments during the ungap algorithm. Default value is 20">
            <validator type="in_range" min="0" />
        </param>        
    </xml>
    <xml name="input_gap_Xdrop">
        <param name="gap_Xdrop" type="integer" value="30" label="Gap Xdrop" help="Xdrop value used to filter alignments during the gap algorithm. Equivalent to blast -X parameter. Default value is 30">
            <validator type="in_range" min="0" />
        </param>        
    </xml>
    <xml name="input_final_gap_Xdrop">
        <param name="final_gap_Xdrop" type="integer" value="100" label="Final gap Xdrop" help="Xdrop value used to filter alignments during the final gap algorithm. Equivalent to blast -Z parameter. . Default value is 100">
            <validator type="in_range" min="0" />
        </param>        
    </xml>

    <token name="@PLAST_DB_SUBJECT_PROT@">
#if $db_opts.db_opts_selector == "db":
  #set $filesystem_path = $db_opts.database.fields.path
  #set $filesystem_path_pin = $filesystem_path + '.pin'
  #set $filesystem_path_pal = $filesystem_path + '.pal'
  #set $exists = os.path.exists( $filesystem_path_pal )
  #if $exists:
    -d "$filesystem_path_pal"
  #else:
    -d "$filesystem_path_pin"
  #end if
#elif $db_opts.db_opts_selector == "histdb":
  #set $filesystem_path = os.path.join($db_opts.histdb.extra_files_path,'blastdb')
  #set $filesystem_path_pin = $filesystem_path + '.pin'
  #set $filesystem_path_pal = $filesystem_path + '.pal'
  #set $exists = os.path.exists( $filesystem_path_pal )
  #if $exists:
    -d "$filesystem_path_pal"
  #else:
    -d "$filesystem_path_pin"
  #end if
#else:
  -d "$db_opts.subject"
#end if
    </token>

    <token name="@PLAST_DB_SUBJECT_NUCL@">
#if $db_opts.db_opts_selector == "db":
  #set $filesystem_path = $db_opts.database.fields.path
  #set $filesystem_path_nin = $filesystem_path + '.nin'
  #set $filesystem_path_nal = $filesystem_path + '.nal'
  #set $exists = os.path.exists( $filesystem_path_nal )
  #if $exists:
    -d "$filesystem_path_nal"
  #else:
    -d "$filesystem_path_nin"
  #end if
#elif $db_opts.db_opts_selector == "histdb":
  #set $filesystem_path = os.path.join($db_opts.histdb.extra_files_path,'blastdb')
  #set $filesystem_path_nin = $filesystem_path + '.nin'
  #set $filesystem_path_nal = $filesystem_path + '.nal'
  #set $exists = os.path.exists( $filesystem_path_nal )
  #if $exists:
    -d "$filesystem_path_nal"
  #else:
    -d "$filesystem_path_nin"
  #end if
#else:
  -d "$db_opts.subject"
#end if
    </token>

    <token name="@BASIC_PARAMS@">
## Need int(str(...)) because $max_hits_query is an InputValueWrapper object not a string
#if (str($max_hits_query) and int(str($max_hits_query)) > 0):
-max-hit-per-query $max_hits_query
#end if
#if (str($max_hsp_hits) and int(str($max_hsp_hits)) > 0):
-max-hsp-per-hit $max_hsp_hits
#end if
    </token>
    <!-- @ON_DB_SUBJECT@ is for use with @BLAST_DB_SUBJECT@ -->
    <token name="@ON_DB_SUBJECT@">
#if str($db_opts.db_opts_selector)=='db'
${db_opts.database}
#elif str($db_opts.db_opts_selector)=='histdb'
${db_opts.histdb.name}
#else
${db_opts.subject.name}
#end if</token>
    <token name="@SEARCH_TIME_WARNING@">.. class:: warningmark

**Note**. Database searches may take a substantial amount of time.
For large input datasets it is advisable to allow overnight processing.  

-----
    </token>
    <token name="@FASTA_WARNING@">.. class:: warningmark

In most cases you should instead turn the other FASTA file into a
database first using *makeblastdb* and search against that.
    </token>
    <token name="@OUTPUT_FORMAT@">
**Output format**

Because Galaxy focuses on processing tabular data, the default output of this
tool is tabular. The standard PLAST tabular output is similar as BLAST+ tabular format, 
it contains 12 columns:

====== ========= ============================================
Column NCBI name Description
------ --------- --------------------------------------------
     1 qseqid    Query Seq-id (ID of your sequence)
     2 sseqid    Subject Seq-id (ID of the database hit)
     3 pident    Percentage of identical matches
     4 length    Alignment length
     5 mismatch  Number of mismatches
     6 gapopen   Number of gap openings
     7 qstart    Start of alignment in query
     8 qend      End of alignment in query
     9 sstart    Start of alignment in subject (database hit)
    10 send      End of alignment in subject (database hit)
    11 evalue    Expectation value (E-value)
    12 bitscore  Bit score
====== ========= ============================================
    </token>
</macros>