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annotate diamond_view.xml @ 15:409ecbc31558 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
author bgruening
date Thu, 27 Sep 2018 06:29:57 -0400
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15
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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1 <tool id="bg_diamond_view" name="Diamond" version="@VERSION@">
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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="requirements" />
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7 <expand macro="stdio" />
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8 <expand macro="version_command" />
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9 <command><![CDATA[
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10 ## need to link because diamont tries to open dataset_xxx.dat.daa
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11 ln -s '$daa' input.daa &&
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12 diamond
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13 view
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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 <expand macro="output_type_macro" />
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24 <expand macro="hit_filter_macro" />
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25 <param argument="--forwardonly" type="boolean" truevalue="--forwardonly" falsevalue="" checked="false" label="only show alignments of forward strand" help=""/>
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26 </inputs>
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27 <outputs>
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28 <expand macro="output_macro" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="daa" ftype="daa" value="diamond_results.daa" />
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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33 <conditional name="output">
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34 <param name="outfmt" value="5"/>
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35 </conditional>
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36 <conditional name="hit_filter">
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37 <param name="hit_filter_select" value="max"/>
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38 <param name="max_target_seqs" value="1" />
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39 </conditional>
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40 <output name="blast_tabular" file="diamond_results.xml"/>
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41 </test>
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42 <test>
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43 <param name="daa" ftype="daa" value="diamond_results.daa" />
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44 <conditional name="output">
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45 <param name="outfmt" value="6"/>
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46 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/>
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47 </conditional>
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48 <output name="blast_tabular" file="diamond_results.tabular"/>
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49 </test>
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50 <test>
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51 <param name="daa" ftype="daa" value="diamond_results.daa" />
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52 <conditional name="output">
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53 <param name="outfmt" value="101"/>
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54 </conditional>
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55 <conditional name="hit_filter">
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56 <param name="hit_filter_select" value="top"/>
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57 <param name="max_target_seqs" value="1" />
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58 </conditional>
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59 <param name="forwardonly" value="--forwardonly" />
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60 <output name="blast_tabular" file="diamond_results.sam"/>
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61 </test>
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62 </tests>
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63
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64 <help>
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65 <![CDATA[
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66
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67 **What it does**
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68
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69 Converts diamond daa files to multiple other formats.
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70
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71 **Input**
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72
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73 Input data is a daa file.
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74
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75
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76 **Output**
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77
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78 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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79
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80 BLAST tables contain the following columns.
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81
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82 Column Description
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83 1 Query Seq-id (ID of your sequence)
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84 2 Subject Seq-id (ID of the database hit)
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85 3 Percentage of identical matches
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86 4 Alignment length
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87 5 Number of mismatches
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88 6 Number of gap openings
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89 7 Start of alignment in query
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90 8 End of alignment in query
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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91 9 Start of alignment in subject (database hit)
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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92 10 End of alignment in subject (database hit)
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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93 11 Expectation value (E-value)
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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94 12 Bit score
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
parents:
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95 ]]>
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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96 </help>
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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97 <expand macro="citations" />
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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98 </tool>