Mercurial > repos > galaxyp > blast_plus_remote_blastp

comparison tools/blast_plus_remote_blastp.xml @ 1:db990c5edc14

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author galaxyp
date Wed, 01 Oct 2014 20:52:17 -0400
parents 820c41bff462
children 9f369b905447
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0:820c41bff462 1:db990c5edc14
1 <tool id="blast_plus_remote_blastp" name="NCBI BLAST+ remote blastp" version="1.0"> 1 <tool id="blast_plus_remote_blastp" name="NCBI BLAST+ remote blastp" version="1.0">
2 <description>Search protein database with protein query sequence(s)</description> 2 <description>Search protein database with protein query sequence(s)</description>
3 <!-- If job splitting is enabled, break up the query file into four (This only works if output is tabular) -->
4 <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism> 3 <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
5 <version_command>blastp -version</version_command> 4 <version_command>blastp -version</version_command>
6 <requirements> 5 <requirements>
7 <requirement type="package" version="333">binaries_for_blast_plus</requirement> 6 <requirement type="package" version="333">binaries_for_blast_plus</requirement>
8 </requirements> 7 </requirements>
175 <option value="basic" selected="True">Hide Advanced Options</option> 174 <option value="basic" selected="True">Hide Advanced Options</option>
176 <option value="advanced">Show Advanced Options</option> 175 <option value="advanced">Show Advanced Options</option>
177 </param> 176 </param>
178 <when value="basic" /> 177 <when value="basic" />
179 <when value="advanced"> 178 <when value="advanced">
180 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
181 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" /> 179 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" />
182 <conditional name="scoring"> 180 <conditional name="scoring">
183 <param name="matrix" type="select" label="Scoring matrix"> 181 <param name="matrix" type="select" label="Scoring matrix">
184 <option value="BLOSUM90">BLOSUM90</option> 182 <option value="BLOSUM90">BLOSUM90</option>
185 <option value="BLOSUM80">BLOSUM80</option> 183 <option value="BLOSUM80">BLOSUM80</option>
310 <option value="-gapopen 10 -gapextend 1">Existense: 10 Extension: 1</option> 308 <option value="-gapopen 10 -gapextend 1">Existense: 10 Extension: 1</option>
311 <option value="-gapopen 9 -gapextend 1" selected="true">Existense: 9 Extension: 1 (default)</option> 309 <option value="-gapopen 9 -gapextend 1" selected="true">Existense: 9 Extension: 1 (default)</option>
312 <option value="-gapopen 8 -gapextend 1">Existense: 8 Extension: 1</option> 310 <option value="-gapopen 8 -gapextend 1">Existense: 8 Extension: 1</option>
313 </param> 311 </param>
314 </when> 312 </when>
315 <!--
316 Can't use '-ungapped' on its own, error back is:
317 Composition-adjusted searched are not supported with an ungapped search, please add -comp_based_stats F or do a gapped search
318 Tried using '-ungapped -comp_based_stats F' and blastp crashed with 'Attempt to access NULL pointer.'
319 <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped -comp_based_stats F" falsevalue="" checked="false" />
320 -->
321 </conditional> 313 </conditional>
322 314
323 <!-- I'd like word_size to be optional, with minimum 2 for blastp -->
324 <param name="word_size" type="integer" value="" optional="true" label="Word size for wordfinder algorithm" help="Recommended: blastp 3, blastp-short 2"> 315 <param name="word_size" type="integer" value="" optional="true" label="Word size for wordfinder algorithm" help="Recommended: blastp 3, blastp-short 2">
325 <validator type="in_range" min="2" /> 316 <validator type="in_range" min="2" />
326 </param> 317 </param>
327 <param name="window_size" type="integer" value="" optional="true" label="Multiple hits window size, use 0 to specify 1-hit algorithm." help="Recommended: blastp 40, blastp-short 15"> 318 <param name="window_size" type="integer" value="" optional="true" label="Multiple hits window size, use 0 to specify 1-hit algorithm." help="Recommended: blastp 40, blastp-short 15">
328 <validator type="in_range" min="0" /> 319 <validator type="in_range" min="0" />