comparison tools/blast_plus_remote_blastp.xml @ 1:db990c5edc14

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0:820c41bff462

<tool id="blast_plus_remote_blastp" name="NCBI BLAST+ remote blastp" version="1.0">
    <description>Search protein database with protein query sequence(s)</description>
    <!-- If job splitting is enabled, break up the query file into four (This only works if output is tabular) -->
    <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
    <version_command>blastp -version</version_command>
    <requirements>
        <requirement type="package" version="333">binaries_for_blast_plus</requirement>
    </requirements>

              <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" />
                <conditional name="scoring">
                    <param name="matrix" type="select" label="Scoring matrix">
                        <option value="BLOSUM90">BLOSUM90</option>
                        <option value="BLOSUM80">BLOSUM80</option>

                            <option value="-gapopen 10 -gapextend 1">Existense: 10  Extension: 1</option>
                            <option value="-gapopen 9 -gapextend 1" selected="true">Existense: 9  Extension: 1 (default)</option>
                            <option value="-gapopen 8 -gapextend 1">Existense: 8  Extension: 1</option>
                        </param>
                    </when>
                <!--
                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 blastp 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" />
                -->
                </conditional>

                <!-- I'd like word_size to be optional, with minimum 2 for blastp -->
                <param name="word_size" type="integer" value="" optional="true" label="Word size for wordfinder algorithm" help="Recommended: blastp 3, blastp-short 2">
                    <validator type="in_range" min="2" />
                </param>
                <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">
                    <validator type="in_range" min="0" />

1:db990c5edc14

<tool id="blast_plus_remote_blastp" name="NCBI BLAST+ remote blastp" version="1.0">
    <description>Search protein database with protein query sequence(s)</description>
    <parallelism method="multi" split_inputs="query" split_mode="number_of_parts" split_size="4" shared_inputs="subject" merge_outputs="output1"></parallelism>
    <version_command>blastp -version</version_command>
    <requirements>
        <requirement type="package" version="333">binaries_for_blast_plus</requirement>
    </requirements>

              <option value="basic" selected="True">Hide Advanced Options</option>
              <option value="advanced">Show Advanced Options</option>
            </param>
            <when value="basic" />
            <when value="advanced">
                <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="false" />
                <conditional name="scoring">
                    <param name="matrix" type="select" label="Scoring matrix">
                        <option value="BLOSUM90">BLOSUM90</option>
                        <option value="BLOSUM80">BLOSUM80</option>

                            <option value="-gapopen 10 -gapextend 1">Existense: 10  Extension: 1</option>
                            <option value="-gapopen 9 -gapextend 1" selected="true">Existense: 9  Extension: 1 (default)</option>
                            <option value="-gapopen 8 -gapextend 1">Existense: 8  Extension: 1</option>
                        </param>
                    </when>
                </conditional>

                <param name="word_size" type="integer" value="" optional="true" label="Word size for wordfinder algorithm" help="Recommended: blastp 3, blastp-short 2">
                    <validator type="in_range" min="2" />
                </param>
                <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">
                    <validator type="in_range" min="0" />