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/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  1<tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.11">
  2    <description>Search protein database with protein query sequence(s)</description>
  3    <version_command>blastp -version</version_command>
  4    <command interpreter="python">hide_stderr.py
  5## The command is a Cheetah template which allows some Python based syntax.
  6## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
  7blastp
  8-query "$query"
  9#if $db_opts.db_opts_selector == "db":
 10  -db "${db_opts.database.fields.path}"
 11#else:
 12  -subject "$db_opts.subject"
 13#end if
 14-task $blast_type
 15-evalue $evalue_cutoff
 16-out $output1
 17##Set the extended list here so if/when we add things, saved workflows are not affected
 18#if str($out_format)=="ext":
 19    -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen"
 20#else:
 21    -outfmt $out_format
 22#end if
 23-num_threads 8
 24#if $adv_opts.adv_opts_selector=="advanced":
 25$adv_opts.filter_query
 26-matrix $adv_opts.matrix
 27## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
 28## Note -max_target_seqs overrides -num_descriptions and -num_alignments
 29#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
 30-max_target_seqs $adv_opts.max_hits
 31#end if
 32#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
 33-word_size $adv_opts.word_size
 34#end if
 35##Ungapped disabled for now - see comments below
 36##$adv_opts.ungapped
 37$adv_opts.parse_deflines
 38## End of advanced options:
 39#end if
 40    </command>
 41    <inputs>
 42        <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 
 43        <conditional name="db_opts">
 44            <param name="db_opts_selector" type="select" label="Subject database/sequences">
 45              <option value="db" selected="True">BLAST Database</option>
 46              <option value="file">FASTA file</option>
 47            </param>
 48            <when value="db">
 49                <param name="database" type="select" label="Protein BLAST database">
 50                    <options from_file="blastdb_p.loc">
 51                      <column name="value" index="0"/>
 52                      <column name="name" index="1"/>
 53                      <column name="path" index="2"/>
 54                    </options>
 55                </param>
 56                <param name="subject" type="hidden" value="" /> 
 57            </when>
 58            <when value="file">
 59                <param name="database" type="hidden" value="" /> 
 60                <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> 
 61            </when>
 62        </conditional>
 63        <param name="blast_type" type="select" display="radio" label="Type of BLAST">
 64            <option value="blastp">blastp</option>
 65            <option value="blastp-short">blastp-short</option>
 66        </param>
 67        <param name="evalue_cutoff" type="float" size="15" value="0.001" label="Set expectation value cutoff" />
 68        <param name="out_format" type="select" label="Output format">
 69            <option value="6" selected="True">Tabular (standard 12 columns)</option>
 70            <option value="ext">Tabular (extended 24 columns)</option>
 71            <option value="5">BLAST XML</option>
 72            <option value="0">Pairwise text</option>
 73            <option value="0 -html">Pairwise HTML</option>
 74            <option value="2">Query-anchored text</option>
 75            <option value="2 -html">Query-anchored HTML</option>
 76            <option value="4">Flat query-anchored text</option>
 77            <option value="4 -html">Flat query-anchored HTML</option>
 78            <!--
 79            <option value="-outfmt 11">BLAST archive format (ASN.1)</option>
 80            -->
 81        </param>
 82        <conditional name="adv_opts">
 83            <param name="adv_opts_selector" type="select" label="Advanced Options">
 84              <option value="basic" selected="True">Hide Advanced Options</option>
 85              <option value="advanced">Show Advanced Options</option>
 86            </param>
 87            <when value="basic" />
 88            <when value="advanced">
 89                <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
 90                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" />
 91                <param name="matrix" type="select" label="Scoring matrix">
 92                    <option value="BLOSUM90">BLOSUM90</option>
 93                    <option value="BLOSUM80">BLOSUM80</option>
 94                    <option value="BLOSUM62" selected="true">BLOSUM62 (default)</option>
 95                    <option value="BLOSUM50">BLOSUM50</option> 
 96                    <option value="BLOSUM45">BLOSUM45</option>
 97                    <option value="PAM250">PAM250</option>
 98                    <option value="PAM70">PAM70</option>
 99                    <option value="PAM30">PAM30</option>
100                </param>
101                <!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer -->
102                <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits">
103                    <validator type="in_range" min="0" />
104                </param>
105                <!-- I'd like word_size to be optional, with minimum 2 for blastp -->
106                <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2.">
107                    <validator type="in_range" min="0" />
108                </param>
109                <!--
110                Can't use '-ungapped' on its own, error back is:
111                Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
112                Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.'
113                <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
114                -->
115                <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"/>
116            </when>
117        </conditional>
118    </inputs>
119    <outputs>
120        <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}">
121            <change_format>
122                <when input="out_format" value="0" format="txt"/>
123                <when input="out_format" value="0 -html" format="html"/>
124                <when input="out_format" value="2" format="txt"/>
125                <when input="out_format" value="2 -html" format="html"/>
126                <when input="out_format" value="4" format="txt"/>
127                <when input="out_format" value="4 -html" format="html"/>
128                <when input="out_format" value="5" format="blastxml"/>
129            </change_format>
130        </data>
131    </outputs>
132    <requirements>
133        <requirement type="binary">blastp</requirement>
134    </requirements>
135    <tests>
136        <test>
137            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
138            <param name="db_opts_selector" value="file" />
139            <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
140            <param name="database" value="" />
141            <param name="evalue_cutoff" value="1e-8" />
142            <param name="blast_type" value="blastp" />
143            <param name="out_format" value="5" />
144            <param name="adv_opts_selector" value="advanced" />
145            <param name="filter_query" value="False" />
146            <param name="matrix" value="BLOSUM62" />
147            <param name="max_hits" value="0" />
148            <param name="word_size" value="0" />
149            <param name="parse_deflines" value="True" />
150            <output name="output1" file="blastp_four_human_vs_rhodopsin.xml" ftype="blastxml" />
151        </test>
152        <test>
153            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
154            <param name="db_opts_selector" value="file" />
155            <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
156            <param name="database" value="" />
157            <param name="evalue_cutoff" value="1e-8" />
158            <param name="blast_type" value="blastp" />
159            <param name="out_format" value="6" />
160            <param name="adv_opts_selector" value="advanced" />
161            <param name="filter_query" value="False" />
162            <param name="matrix" value="BLOSUM62" />
163            <param name="max_hits" value="0" />
164            <param name="word_size" value="0" />
165            <param name="parse_deflines" value="True" />
166            <output name="output1" file="blastp_four_human_vs_rhodopsin.tabular" ftype="tabular" />
167        </test>
168        <test>
169            <param name="query" value="four_human_proteins.fasta" ftype="fasta" />
170            <param name="db_opts_selector" value="file" />
171            <param name="subject" value="rhodopsin_proteins.fasta" ftype="fasta" />
172            <param name="database" value="" />
173            <param name="evalue_cutoff" value="1e-8" />
174            <param name="blast_type" value="blastp" />
175            <param name="out_format" value="ext" />
176            <param name="adv_opts_selector" value="advanced" />
177            <param name="filter_query" value="False" />
178            <param name="matrix" value="BLOSUM62" />
179            <param name="max_hits" value="0" />
180            <param name="word_size" value="0" />
181            <param name="parse_deflines" value="True" />
182            <output name="output1" file="blastp_four_human_vs_rhodopsin_ext.tabular" ftype="tabular" />
183        </test>
184        <test>
185            <param name="query" value="rhodopsin_proteins.fasta" ftype="fasta" />
186            <param name="db_opts_selector" value="file" />
187            <param name="subject" value="four_human_proteins.fasta" ftype="fasta" />
188            <param name="database" value="" />
189            <param name="evalue_cutoff" value="1e-8" />
190            <param name="blast_type" value="blastp" />
191            <param name="out_format" value="6" />
192            <param name="adv_opts_selector" value="basic" />
193            <output name="output1" file="blastp_rhodopsin_vs_four_human.tabular" ftype="tabular" />
194        </test>
195    </tests>
196    <help>
197    
198.. class:: warningmark
199
200**Note**. Database searches may take a substantial amount of time.
201For large input datasets it is advisable to allow overnight processing.  
202
203-----
204
205**What it does**
206
207Search a *protein database* using a *protein query*,
208using the NCBI BLAST+ blastp command line tool.
209
210-----
211
212**Output format**
213
214Because Galaxy focuses on processing tabular data, the default output of this
215tool is tabular. The standard BLAST+ tabular output contains 12 columns:
216
217====== ========= ============================================
218Column NCBI name Description
219------ --------- --------------------------------------------
220     1 qseqid    Query Seq-id (ID of your sequence)
221     2 sseqid    Subject Seq-id (ID of the database hit)
222     3 pident    Percentage of identical matches
223     4 length    Alignment length
224     5 mismatch  Number of mismatches
225     6 gapopen   Number of gap openings
226     7 qstart    Start of alignment in query
227     8 qend      End of alignment in query
228     9 sstart    Start of alignment in subject (database hit)
229    10 send      End of alignment in subject (database hit)
230    11 evalue    Expectation value (E-value)
231    12 bitscore  Bit score
232====== ========= ============================================
233
234The BLAST+ tools can optionally output additional columns of information,
235but this takes longer to calculate. Most (but not all) of these columns are
236included by selecting the extended tabular output. The extra columns are
237included *after* the standard 12 columns. This is so that you can write
238workflow filtering steps that accept either the 12 or 24 column tabular
239BLAST output.
240
241====== ============= ===========================================
242Column NCBI name     Description
243------ ------------- -------------------------------------------
244    13 sallseqid     All subject Seq-id(s), separated by a ';'
245    14 score         Raw score
246    15 nident        Number of identical matches
247    16 positive      Number of positive-scoring matches
248    17 gaps          Total number of gaps
249    18 ppos          Percentage of positive-scoring matches
250    19 qframe        Query frame
251    20 sframe        Subject frame
252    21 qseq          Aligned part of query sequence
253    22 sseq          Aligned part of subject sequence
254    23 qlen          Query sequence length
255    24 slen          Subject sequence length
256====== ============= ===========================================
257
258The third option is BLAST XML output, which is designed to be parsed by
259another program, and is understood by some Galaxy tools.
260
261You can also choose several plain text or HTML output formats which are designed to be read by a person (not by another program).
262The HTML versions use basic webpage formatting and can include links to the hits on the NCBI website.
263The pairwise output (the default on the NCBI BLAST website) shows each match as a pairwise alignment with the query.
264The two query anchored outputs show a multiple sequence alignment between the query and all the matches,
265and differ in how insertions are shown (marked as insertions or with gap characters added to the other sequences).
266
267-------
268
269**References**
270
271Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
272
273Schaffer et al. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. 2001. Nucleic Acids Res. 29:2994-3005.
274
275    </help>
276</tool>