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annotate diamond_view.xml @ 21:3f75f7bc764d draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b2634d43c65880b8450221276487b3198a8fe03c
author iuc
date Tue, 10 Jun 2025 13:51:43 +0000
parents 0729ae1533e5
children
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1 <tool id="bg_diamond_view" name="Diamond view" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2" license="GPL-3.0">
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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 detect_errors="aggressive"><![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 --threads \${GALAXY_SLOTS:-1}
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15 --daa input.daa
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16 @OUTPUT_ARGS@
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17 @HITFILTER_ARGS@
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18 $forwardonly
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19 --verbose
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20 ]]>
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21 </command>
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22 <inputs>
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23 <param argument="--daa" type="data" format="daa" label="input file in DAA format"/>
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24 <section name="output_section" title="Output options">
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25 <expand macro="output_type_macro"/>
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26 </section>
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27 <expand macro="hit_filter_macro"/>
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28 <param argument="--forwardonly" type="boolean" truevalue="--forwardonly" falsevalue="" checked="false" label="only show alignments of forward strand"/>
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29 </inputs>
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30 <outputs>
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31 <expand macro="output_macro"/>
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32 </outputs>
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33 <tests>
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34 <test expect_num_outputs="1">
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35 <param name="daa" ftype="daa" value="diamond_results.daa"/>
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36 <section name="output_section">
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37 <conditional name="output">
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38 <param name="outfmt" value="5"/>
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39 </conditional>
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40 </section>
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41 <conditional name="hit_filter">
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42 <param name="hit_filter_select" value="max"/>
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43 <param name="max_target_seqs" value="1"/>
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44 </conditional>
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45 <output name="blast_tabular" file="diamond_results.xml"/>
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46 </test>
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47 <test expect_num_outputs="1">
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48 <param name="daa" ftype="daa" value="diamond_results.daa"/>
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49 <section name="output_section">
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50 <conditional name="output">
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51 <param name="outfmt" value="6"/>
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52 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore,cigar,scovhsp"/>
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53 </conditional>
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54 </section>
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55 <output name="blast_tabular" file="diamond_view_results.tabular"/>
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56 </test>
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57 <test expect_num_outputs="1">
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58 <param name="daa" ftype="daa" value="diamond_results.daa"/>
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59 <section name="output_section">
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60 <conditional name="output">
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61 <param name="outfmt" value="101"/>
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62 </conditional>
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63 </section>
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64 <conditional name="hit_filter">
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65 <param name="hit_filter_select" value="top"/>
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66 <param name="max_target_seqs" value="1"/>
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67 </conditional>
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68 <param name="forwardonly" value="--forwardonly"/>
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69 <output name="blast_tabular" file="diamond_results.sam" lines_diff="2"/>
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70 </test>
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71 </tests>
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72 <help>
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73 <![CDATA[
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74
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75 **What it does**
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76
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77 Converts diamond daa files to multiple other formats.
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79 **Input**
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81 Input data is a daa file.
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83
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84 **Output**
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85
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86 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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88 BLAST tables contain the following columns.
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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89
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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90 Column Description
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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91 1 Query Seq-id (ID of your sequence)
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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92 2 Subject Seq-id (ID of the database hit)
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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93 3 Percentage of identical matches
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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94 4 Alignment length
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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95 5 Number of mismatches
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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96 6 Number of gap openings
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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97 7 Start of alignment in query
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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98 8 End of alignment in query
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
bgruening
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99 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
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100 10 End of alignment in subject (database hit)
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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101 11 Expectation value (E-value)
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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102 12 Bit score
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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103 ]]>
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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104 </help>
20
0729ae1533e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
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105 <expand macro="citations"/>
15
409ecbc31558 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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106 </tool>