Mercurial > repos > iuc > mash_dist

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash commit ff9564c2e6924fab084b6e02a3a196650041636a
author iuc
date Thu, 16 Oct 2025 16:42:27 +0000
parents 58c5e5a3f5cb
children
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58c5e5a3f5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
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1 <tool id="mash_dist" name="mash dist" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
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2 <description>Estimate distance between query sequences</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="xref"/>
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7 <expand macro="requirements"/>
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8 <expand macro="version_command"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 #set REFERENCE = "reference."+$reference.ext
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11 #set QUERY = "query."+$query.ext
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12 ln -s '$reference' $REFERENCE &&
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13 ln -s '$query' $QUERY &&
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14 mash dist
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15 #if $table_output:
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16 -t
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17 #end if
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18 -p \${GALAXY_SLOTS:-1}
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19 #if $pvalue:
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20 -v $pvalue
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21 #end if
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22 #if $distance:
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23 -d $distance
58c5e5a3f5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
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24 #end if
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25 $REFERENCE
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26 $QUERY
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27 > '$output'
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28 ]]></command>
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29 <inputs>
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30 <param name="table_output" type="boolean" truevalue="-t" falsevalue="" checked="true" label="Table output?" help="Will not report p-values, but fields will be blank if they do not meet the p-value threshold"/>
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31 <param name="reference" type="data" format="@INTYPES@,msh" label="Reference"/>
58c5e5a3f5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
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32 <param name="query" type="data" format="@INTYPES@,msh" label="Query"/>
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33 <param name="pvalue" type="float" argument="-v" value="1.0" min="0" max="1.0" label=" Maximum p-value"/>
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34 <param name="distance" type="float" argument="-d" value="1.0" min="0" max="1.0" label="Maximum distance"/>
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35 </inputs>
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36 <outputs>
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37 <data name="output" format="tsv" label="${tool.name} on ${on_string}"/>
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38 </outputs>
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39 <tests>
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40 <test expect_num_outputs="1">
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41 <param name="table_output" value="true"/>
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42 <param name="reference" value="ERR024951_seqtk_sample_1000_1.fastq" ftype="fastqsanger"/>
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43 <param name="query" value="ERR024951_seqtk_sample_1000_2.fastq" ftype="fastqsanger"/>
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44 <output name="output">
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45 <assert_contents>
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46 <has_text text="0.203604"/>
58c5e5a3f5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
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47 </assert_contents>
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48 </output>
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49 </test>
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50 <test expect_num_outputs="1">
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51 <param name="table_output" value="true"/>
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52 <param name="reference" value="ERR024951_seqtk_sample_1000_1.fastq.gz" ftype="fastqsanger.gz"/>
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53 <param name="query" value="ERR024951_seqtk_sample_1000_2.fastq.gz" ftype="fastqsanger.gz"/>
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54 <output name="output">
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55 <assert_contents>
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56 <has_text text="0.203604"/>
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57 </assert_contents>
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58 </output>
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59 </test>
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60 <test expect_num_outputs="1">
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61 <param name="table_output" value="true"/>
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62 <param name="reference" value="test_06_mash_sketch.msh" ftype="msh"/>
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63 <param name="query" value="test_07_mash_sketch.msh" ftype="msh"/>
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64 <output name="output">
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65 <assert_contents>
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66 <has_text text="1"/>
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67 </assert_contents>
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68 </output>
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69 </test>
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70 <test expect_num_outputs="1">
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71 <param name="table_output" value="true"/>
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72 <param name="reference" value="m64326e_231117_100511.hifi_reads.bc2068--bc2068.msh" ftype="msh"/>
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73 <param name="query" value="m64326e_231130_052019.hifi_reads.bc2068--bc2068.msh" ftype="msh"/>
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74 <output name="output">
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75 <assert_contents>
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76 <has_text text="0.0149234"/>
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77 </assert_contents>
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78 </output>
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79 </test>
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80 </tests>
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81 <help><![CDATA[
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82
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83 **What it does**
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84
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85 Estimate the distance of each query sequence to the reference. Both the
58c5e5a3f5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
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86 reference and queries can be fasta or fastq, gzipped or not, or Mash sketch
58c5e5a3f5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
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87 files (.msh) with matching k-mer sizes. Query files can also be files of file
58c5e5a3f5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
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88 names (see -l). Whole files are compared by default (see -i). The output
58c5e5a3f5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
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89 fields are [reference-ID, query-ID, distance, p-value, shared-hashes].
58c5e5a3f5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
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90
58c5e5a3f5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
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91 ]]></help>
58c5e5a3f5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
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92 <expand macro="citations"/>
58c5e5a3f5cb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 38a8594d05b6a2fc57db891858b789735dc4a8c3
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93 </tool>