--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,286 @@
+<tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.11">
+    <description>Search translated nucleotide database with protein query sequence(s)</description>
+    <version_command>tblastn -version</version_command>
+    <command interpreter="python">hide_stderr.py
+## The command is a Cheetah template which allows some Python based syntax.
+## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
+tblastn
+-query "$query"
+#if $db_opts.db_opts_selector == "db":
+  -db "${db_opts.database.fields.path}"
+#else:
+  -subject "$db_opts.subject"
+#end if
+-evalue $evalue_cutoff
+-out $output1
+##Set the extended list here so if/when we add things, saved workflows are not affected
+#if str($out_format)=="ext":
+    -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
+#else:
+    -outfmt $out_format
+#end if
+-num_threads 8
+#if $adv_opts.adv_opts_selector=="advanced":
+$adv_opts.filter_query
+-matrix $adv_opts.matrix
+## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
+## Note -max_target_seqs overrides -num_descriptions and -num_alignments
+#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
+-max_target_seqs $adv_opts.max_hits
+#end if
+#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
+-word_size $adv_opts.word_size
+#end if
+##Ungapped disabled for now - see comments below
+##$adv_opts.ungapped
+$adv_opts.parse_deflines
+## End of advanced options:
+#end if
+    </command>
+    <inputs>
+        <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 
+        <conditional name="db_opts">
+            <param name="db_opts_selector" type="select" label="Subject database/sequences">
+              <option value="db" selected="True">BLAST Database</option>
+              <option value="file">FASTA file</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="subject" type="hidden" value="" /> 
+            </when>
+            <when value="file">
+                <param name="database" type="hidden" value="" /> 
+                <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> 
+            </when>
+        </conditional>
+        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
+        <param name="out_format" type="select" label="Output format">
+            <option value="6" selected="True">Tabular (standard 12 columns)</option>
+            <option value="ext">Tabular (extended 24 columns)</option>
+            <option value="5">BLAST XML</option>
+            <option value="0">Pairwise text</option>
+            <option value="0 -html">Pairwise HTML</option>
+            <option value="2">Query-anchored text</option>
+            <option value="2 -html">Query-anchored HTML</option>
+            <option value="4">Flat query-anchored text</option>
+            <option value="4 -html">Flat query-anchored HTML</option>
+            <!--
+            <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
+            -->
+        </param>
+        <conditional name="adv_opts">
+            <param name="adv_opts_selector" type="select" label="Advanced Options">
+              <option value="basic" selected="True">Hide Advanced Options</option>
+              <option value="advanced">Show Advanced Options</option>
+            </param>
+            <when value="basic" />
+            <when value="advanced">
+                <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
+                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
+                <param name="matrix" type="select" label="Scoring matrix">
+                    <option value="BLOSUM90">BLOSUM90</option>
+                    <option value="BLOSUM80">BLOSUM80</option>
+                    <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
+                    <option value="BLOSUM50">BLOSUM50</option> 
+                    <option value="BLOSUM45">BLOSUM45</option>
+                    <option value="PAM250">PAM250</option>
+                    <option value="PAM70">PAM70</option>
+                    <option value="PAM30">PAM30</option>
+                </param>
+                <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
+                <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
+                    <validator type="in_range" min="0" />
+                </param>
+                <!-- I'd like word_size to be optional, with minimum 2 for blastp -->
+                <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
+                    <validator type="in_range" min="0" />
+                </param>
+                <!--
+                Can't use '-ungapped' on its own, error back is:
+                Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
+                Tried using '-ungapped -comp_based_stats F' and tblastn crashed with 'Attempt to access NULL pointer.'
+                <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
+                -->
+                <param name="parse_deflines" type="boolean" label="Should the query and subject defline(s) be parsed?" truevalue="-parse_deflines" falsevalue="" checked="false" help="This affects the formatting of the query/subject ID strings"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}">
+            <change_format>
+                <when input="out_format" value="0" format="txt"/>
+                <when input="out_format" value="0 -html" format="html"/>
+                <when input="out_format" value="2" format="txt"/>
+                <when input="out_format" value="2 -html" format="html"/>
+                <when input="out_format" value="4" format="txt"/>
+                <when input="out_format" value="4 -html" format="html"/>
+                <when input="out_format" value="5" format="blastxml"/>
+            </change_format>
+        </data>
+    </outputs>
+    <requirements>
+        <requirement type="binary">tblastn</requirement>
+    </requirements>
+    <tests>
+        <test>
+            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
+            <param name="db_opts_selector" value="file" />
+            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
+            <param name="database" value="" />
+            <param name="evalue_cutoff" value="1e-10" />
+            <param name="out_format" value="5" />
+            <param name="adv_opts_selector" value="advanced" />
+            <param name="filter_query" value="false" />
+            <param name="matrix" value="BLOSUM80" />
+            <param name="max_hits" value="0" />
+            <param name="word_size" value="0" />
+            <param name="parse_deflines" value="false" />
+            <output name="output1" file="tblastn_four_human_vs_rhodopsin.xml" ftype="blastxml" />
+        </test>
+        <test>
+            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
+            <param name="db_opts_selector" value="file" />
+            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
+            <param name="database" value="" />
+            <param name="evalue_cutoff" value="1e-10" />
+            <param name="out_format" value="ext" />
+            <param name="adv_opts_selector" value="advanced" />
+            <param name="filter_query" value="false" />
+            <param name="matrix" value="BLOSUM80" />
+            <param name="max_hits" value="0" />
+            <param name="word_size" value="0" />
+            <param name="parse_deflines" value="false" />
+            <output name="output1" file="tblastn_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
+            <param name="db_opts_selector" value="file" />
+            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
+            <param name="database" value="" />
+            <param name="evalue_cutoff" value="1e-10" />
+            <param name="out_format" value="6" />
+            <param name="adv_opts_selector" value="advanced" />
+            <param name="filter_query" value="false" />
+            <param name="matrix" value="BLOSUM80" />
+            <param name="max_hits" value="0" />
+            <param name="word_size" value="0" />
+            <param name="parse_deflines" value="false" />
+            <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <!-- Same as above, but parse deflines - on BLAST 2.2.25+ makes no difference -->
+            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
+            <param name="db_opts_selector" value="file" />
+            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
+            <param name="database" value="" />
+            <param name="evalue_cutoff" value="1e-10" />
+            <param name="out_format" value="6" />
+            <param name="adv_opts_selector" value="advanced" />
+            <param name="filter_query" value="false" />
+            <param name="matrix" value="BLOSUM80" />
+            <param name="max_hits" value="0" />
+            <param name="word_size" value="0" />
+            <param name="parse_deflines" value="true" />
+            <output name="output1" file="tblastn_four_human_vs_rhodopsin.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
+            <param name="db_opts_selector" value="file" />
+            <param name="subject" value="rhodopsin_nucs.fasta" ftype="fasta" />
+            <param name="database" value="" />
+            <param name="evalue_cutoff" value="1e-10" />
+            <param name="out_format" value="0 -html" />
+            <param name="adv_opts_selector" value="advanced" />
+            <param name="filter_query" value="false" />
+            <param name="matrix" value="BLOSUM80" />
+            <param name="max_hits" value="0" />
+            <param name="word_size" value="0" />
+            <param name="parse_deflines" value="false" />
+            <output name="output1" file="tblastn_four_human_vs_rhodopsin.html" ftype="html" />
+        </test>
+    </tests>
+    <help>
+    
+.. class:: warningmark
+
+**Note**. Database searches may take a substantial amount of time.
+For large input datasets it is advisable to allow overnight processing.  
+
+-----
+
+**What it does**
+
+Search a *translated nucleotide database* using a *protein query*,
+using the NCBI BLAST+ tblastn command line tool.
+
+-----
+
+**Output format**
+
+Because Galaxy focuses on processing tabular data, the default output of this
+tool is tabular. The standard BLAST+ tabular output 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
+====== ========= ============================================
+
+The BLAST+ tools can optionally output additional columns of information,
+but this takes longer to calculate. Most (but not all) of these columns are
+included by selecting the extended tabular output. The extra columns are
+included *after* the standard 12 columns. This is so that you can write
+workflow filtering steps that accept either the 12 or 24 column tabular
+BLAST output.
+
+====== ============= ===========================================
+Column NCBI name     Description
+------ ------------- -------------------------------------------
+    13 sallseqid     All subject Seq-id(s), separated by a ';'
+    14 score         Raw score
+    15 nident        Number of identical matches
+    16 positive      Number of positive-scoring matches
+    17 gaps          Total number of gaps
+    18 ppos          Percentage of positive-scoring matches
+    19 qframe        Query frame
+    20 sframe        Subject frame
+    21 qseq          Aligned part of query sequence
+    22 sseq          Aligned part of subject sequence
+    23 qlen          Query sequence length
+    24 slen          Subject sequence length
+====== ============= ===========================================
+
+The third option is BLAST XML output, which is designed to be parsed by
+another program, and is understood by some Galaxy tools.
+
+You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
+The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
+The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
+The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
+and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
+
+-------
+
+**References**
+
+Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
+
+    </help>
+</tool>