Mercurial > repos > bgruening > diamond

annotate diamond_view.xml @ 10:1e3323a44643 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
author iuc
date Fri, 22 Apr 2022 13:51:34 +0000
parents f921014aba5a
children
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rev   line source
10
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
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1 <tool id="bg_diamond_view" name="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="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[
7
62c9df8382c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
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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
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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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 --compress '0'
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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>
6
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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" help=""/>
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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"/>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
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39 </conditional>
1e3323a44643 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
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40 </section>
6
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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>
9
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47 <test expect_num_outputs="1">
6
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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>
8
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55 <output name="blast_tabular" file="diamond_view_results.tabular"/>
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56 </test>
9
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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>
6
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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"/>
6
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70 </test>
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71 </tests>
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72
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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73 <help>
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74 <![CDATA[
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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75
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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76 **What it does**
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77
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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78 Converts diamond daa files to multiple other formats.
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79
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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80 **Input**
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81
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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82 Input data is a daa file.
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83
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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84
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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85 **Output**
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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86
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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87 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
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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89 BLAST tables contain the following columns.
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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90
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91 Column Description
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92 1 Query Seq-id (ID of your sequence)
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93 2 Subject Seq-id (ID of the database hit)
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94 3 Percentage of identical matches
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95 4 Alignment length
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96 5 Number of mismatches
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97 6 Number of gap openings
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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98 7 Start of alignment in query
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99 8 End of alignment in query
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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100 9 Start of alignment in subject (database hit)
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101 10 End of alignment in subject (database hit)
64be1ac21109 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
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102 11 Expectation value (E-value)
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103 12 Bit score
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104 ]]>
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105 </help>
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106 <expand macro="citations" />
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107 </tool>