# HG changeset patch
# User peterjc
# Date 1366895113 14400
# Node ID 08be1b2b0bf62b5f27a1ededd118d10a0e6c1d78
# Parent  e77e30f1deebfa33267bfb43678ed2166aab9357
Uploaded v0.0.19 preview take 4, added missing wrapper for RPS-TBLASTN

diff -r e77e30f1deeb -r 08be1b2b0bf6 tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml	Thu Apr 25 09:05:13 2013 -0400
@@ -0,0 +1,237 @@
+<tool id="ncbi_rpstblastn_wrapper" name="NCBI BLAST+ rpstblastn" version="0.0.3">
+    <description>Search protein domain database (PSSMs) with translated nucleotide query sequence(s)</description>
+    <!-- If job splitting is enabled, break up the query file into parts -->
+    <parallelism method="multi" split_inputs="query" split_mode="to_size" split_size="1000" shared_inputs="subject" merge_outputs="output1"></parallelism>
+    <requirements>
+        <requirement type="binary">rpstblastn</requirement>
+        <requirement type="package" version="2.2.26+">blast+</requirement>
+    </requirements>
+    <version_command>rpstblastn -version</version_command>
+    <command>
+## The command is a Cheetah template which allows some Python based syntax.
+## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
+rpstblastn
+-query "$query"
+#if $db_opts.db_opts_selector == "db":
+  -db "${db_opts.database.fields.path}"
+#elif $db_opts.db_opts_selector == "histdb":
+  -db "${os.path.join($db_opts.histdb.extra_files_path,'blastdb')}"
+#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
+##Seems rpstblastn does not currently support multiple threads :(
+##-num_threads 8
+#if $adv_opts.adv_opts_selector=="advanced":
+$adv_opts.filter_query
+## 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 $adv_opts.word_size
+#end if
+$adv_opts.parse_deflines
+## End of advanced options:
+#end if
+    </command>
+    <stdio>
+        <!-- Anything other than zero is an error -->
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <!-- In case the return code has not been set propery check stderr too -->
+        <regex match="Error:" />
+        <regex match="Exception:" />
+    </stdio>
+    <inputs>
+        <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
+        <conditional name="db_opts">
+            <param name="db_opts_selector" type="select" label="Protein domain database (PSSM)">
+              <option value="db" selected="True">Locally installed BLAST database</option>
+              <!-- TODO - define new datatype
+              <option value="histdb">BLAST protein domain database from your history</option>
+              -->
+            </param>
+            <when value="db">
+                <param name="database" type="select" label="Protein domain database">
+                    <options from_file="blastdb_d.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>
+            <!-- TODO - define new datatype
+            <when value="histdb">
+                <param name="database" type="hidden" value="" />
+                <param name="histdb" type="data" format="blastdbd" label="Protein domain database" />
+                <param name="subject" type="hidden" value="" />
+            </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">Tabular (standard 12 columns)</option>
+            <option value="ext" selected="True">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="false" />
+                <!-- 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 rpsblast -->
+                <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>
+                <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="RPS-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>
+    <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 *protein domain database* using a *nucleotide query*,
+using the NCBI BLAST+ rpstblastn command line tool.
+
+The protein domain databases use position-specific scoring matrices
+(PSSMs) and are available for a number of domain collections including:
+
+*CDD* - NCBI curarated meta-collection of domains, see
+http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#NCBI_curated_domains
+
+*Kog* - PSSMs from automatically aligned sequences and sequence
+fragments classified in the KOGs resource, the eukaryotic 
+counterpart to COGs, see http://www.ncbi.nlm.nih.gov/COG/new/
+
+*Cog* - PSSMs from automatically aligned sequences and sequence
+fragments classified in the COGs resource, which focuses primarily
+on prokaryotes, see http://www.ncbi.nlm.nih.gov/COG/new/
+
+*Pfam* - PSSMs from Pfam-A seed alignment database, see
+http://pfam.sanger.ac.uk/
+
+*Smart* - PSSMs from SMART domain alignment database, see
+http://smart.embl-heidelberg.de/
+
+*Tigr* - PSSMs from TIGRFAM database of protein families, see
+http://www.jcvi.org/cms/research/projects/tigrfams/overview/
+
+*Prk* - PSSms from automatically aligned stable clusters in the
+Protein Clusters database, see
+http://www.ncbi.nlm.nih.gov/proteinclusters?cmd=search&amp;db=proteinclusters
+
+The exact list of domain databases offered will depend on how your
+local Galaxy has been configured.
+
+-----
+
+**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. Galaxy now uses this extended 24 column output by default.
+
+====== ============= ===========================================
+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**
+
+Marchler-Bauer A, Bryant SH. CD-Search: protein domain annotations on the fly. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W327-31.
+
+    </help>
+</tool>