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1 <tool id="pl_diamond_view" name="PL_Diamond view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="19.01">
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2 <description>generate formatted output from DAA files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="stdio" />
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7 <expand macro="version_command" />
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## need to link because diamont tries to open dataset_xxx.dat.daa
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10 ln -s '$daa' input.daa &&
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11 $/usr/bin/diamond
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12 view
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13 --threads \${GALAXY_SLOTS:-1}
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14 --daa input.daa
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15 @OUTPUT_ARGS@
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16 @HITFILTER_ARGS@
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17 $forwardonly
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18 --compress '0'
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19 ]]>
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20 </command>
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21 <inputs>
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22 <param argument="--daa" type="data" format="daa" label="input file in DAA format" />
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23 <section name="output_section" title="Output options">
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24 <expand macro="output_type_macro" />
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25 </section>
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26 <expand macro="hit_filter_macro" />
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27 <param argument="--forwardonly" type="boolean" truevalue="--forwardonly" falsevalue="" checked="false" label="only show alignments of forward strand" help=""/>
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28 </inputs>
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29 <outputs>
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30 <expand macro="output_macro" />
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31 </outputs>
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32 <help>
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33 <![CDATA[
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34
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35 **What it does**
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36
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37 Converts diamond daa files to multiple other formats.
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38
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39 **Input**
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40
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41 Input data is a daa file.
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42
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43
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44 **Output**
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45
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46 Alignment results in BLAST format (pairwise/tabular), xml, sam, taxonomic (Note the latter does not work with the current diamond version. )
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47
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48 BLAST tables contain the following columns.
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49
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50 Column Description
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51 1 Query Seq-id (ID of your sequence)
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52 2 Subject Seq-id (ID of the database hit)
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53 3 Percentage of identical matches
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54 4 Alignment length
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55 5 Number of mismatches
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56 6 Number of gap openings
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57 7 Start of alignment in query
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58 8 End of alignment in query
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59 9 Start of alignment in subject (database hit)
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60 10 End of alignment in subject (database hit)
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61 11 Expectation value (E-value)
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62 12 Bit score
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63 ]]>
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64 </help>
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65 <expand macro="citations" />
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66 </tool>
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