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1 <tool id="ncbi_blastdbcmd_info" name="NCBI BLAST+ database info" version="0.0.2">
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2 <description>Show BLAST database information from blastdbcmd</description>
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3 <command>
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4 blastdbcmd -dbtype $db_opts.db_type -db "${db_opts.database.fields.path}" -info -out $info
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5 </command>
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6 <stdio>
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7 <!-- Anything other than zero is an error -->
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8 <exit_code range="1:" />
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9 <exit_code range=":-1" />
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10 <!-- Suspect blastdbcmd sometimes fails to set error level -->
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11 <regex match="Error:" />
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12 <regex match="EXception:" />
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13 </stdio>
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14 <inputs>
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15 <conditional name="db_opts">
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16 <param name="db_type" type="select" label="Type of BLAST database">
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17 <option value="nucl" selected="True">Nucleotide</option>
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18 <option value="prot">Protein</option>
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19 </param>
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20 <when value="nucl">
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21 <param name="database" type="select" label="Nucleotide BLAST database">
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22 <options from_file="blastdb.loc">
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23 <column name="value" index="0"/>
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24 <column name="name" index="1"/>
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25 <column name="path" index="2"/>
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26 </options>
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27 </param>
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28 </when>
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29 <when value="prot">
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30 <param name="database" type="select" label="Protein BLAST database">
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31 <options from_file="blastdb_p.loc">
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32 <column name="value" index="0"/>
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33 <column name="name" index="1"/>
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34 <column name="path" index="2"/>
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35 </options>
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36 </param>
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37 </when>
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38 </conditional>
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39 </inputs>
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40 <outputs>
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41 <data name="info" format="txt" label="${db_opts.database.fields.name} info" />
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42 </outputs>
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43 <requirements>
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44 <requirement type="binary">blastdbcmd</requirement>
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45 </requirements>
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46 <help>
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47
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48 **What it does**
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49
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50 Calls the NCBI BLAST+ blastdbcmd command line tool with the -info
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51 switch to give summary information about a BLAST database, such as
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52 the size (number of sequences and total length) and date.
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53
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54 -------
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55
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56 **References**
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57
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58 Altschul et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. 1997. Nucleic Acids Res. 25:3389-3402.
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59
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60 Schaffer 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.
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61
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62 </help>
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63 </tool>
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