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annotate mash_sketch.xml @ 3:43f9ca23c132 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 0412195e7380e34250a231f6ea4371d309284ff9"
author iuc
date Sat, 24 Apr 2021 13:28:53 +0000
parents 91ee99b4f05a
children
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1 <tool id="mash_sketch" name="mash sketch" version="@TOOL_VERSION@+galaxy0" profile="19.01">
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2 <description>
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3 Create a reduced representation of a sequence or set of sequences, based on min-hashes
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="version_command" />
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10 <command detect_errors="exit_code"><![CDATA[
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11 mash sketch
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12 -s '${sketch_size}'
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13 -k '${kmer_size}'
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14 -w '${prob_threshold}'
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15 #if str ( $reads_assembly.reads_assembly_selector ) == "reads"
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16 -m '${reads_assembly.minimum_kmer_copies}'
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17 -r
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18 #if $reads_assembly.target_coverage
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19 -c '${reads_assembly.target_coverage}'
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20 #end if
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21 #if $reads_assembly.genome_size
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22 -g '${reads_assembly.genome_size}'
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23 #end if
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24 #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired"
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25 '$reads_assembly.reads_input.reads_1' '$reads_assembly.reads_input.reads_2'
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26 #end if
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27 #if str( $reads_assembly.reads_input.reads_input_selector ) == "paired_collection"
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28 '$reads_assembly.reads_input.reads.forward' '$reads_assembly.reads_input.reads.reverse'
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29 #end if
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30 #if str( $reads_assembly.reads_input.reads_input_selector ) == "single"
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31 '$reads_assembly.reads_input.reads'
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32 #end if
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33 #elif str ( $reads_assembly.reads_assembly_selector ) == "assembly"
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34 -p \${GALAXY_SLOTS:-1}
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35 '${assembly}'
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36 ${reads_assembly.individual_sequences}
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37 #end if
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38 -o 'sketch'
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39 ]]></command>
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40 <inputs>
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41 <conditional name="reads_assembly">
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42 <param name="reads_assembly_selector" type="select" label="Input: Reads or Assemblies">
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43 <option selected="True" value="reads">Reads</option>
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44 <option value="assembly">Assembly</option>
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45 </param>
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46 <when value="reads">
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47 <conditional name="reads_input">
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48 <param name="reads_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
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49 <option value="paired">Paired</option>
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50 <option value="single">Single</option>
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51 <option value="paired_collection">Paired Collection</option>
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52 </param>
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53 <when value="paired">
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54 <param name="reads_1" type="data" format="@INTYPES@" label="Select first set of reads" help="Specify dataset with forward reads"/>
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55 <param name="reads_2" type="data" format="@INTYPES@" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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56 </when>
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57 <when value="single">
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58 <param name="reads" type="data" format="@INTYPES@" label="Select fastq dataset" help="Specify dataset with single reads"/>
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59 </when>
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60 <when value="paired_collection">
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61 <param name="reads" format="@INTYPES@" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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62 </when>
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63 </conditional>
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64 <param type="integer" name="minimum_kmer_copies" argument="-m" value="1" min="1" max="1000" label="Minimum copies of each k-mer required to pass noise filter"/>
2
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65 <param type="integer" name="target_coverage" argument="-c" value="" min="0" max="500" optional="true" label="Target coverage" help="If specified, sketching will conclude if this coverage is reached before the end of the input file (estimated by average k-mer multiplicity)"/>
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66 <param type="integer" name="genome_size" argument="-g" value="" min="1000" max="100000000000" optional="true" label="Genome size" help="If specified, will be used for p-value calculation instead of an estimated size from k-mer content"/>
0
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67 </when>
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68 <when value="assembly">
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69 <param name="assembly" type="data" format="fasta,fasta.gz" label="Assembly"/>
2
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70 <param type="boolean" name="individual_sequences" truevalue="-i" falsevalue="" label="Sketch individual Sequences" help="Sketch individual sequences, rather than whole files, e.g. for multi-fastas of single-chromosome genomes or pair-wise gene comparisons"/>
0
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71 </when>
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72 </conditional>
2
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73 <param type="integer" name="sketch_size" argument="-s" value="1000" min="10" max="1000000" label="Sketch size" help="Each sketch will have at most this many non-redundant min-hashes"/>
0
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74 <param type="integer" name="kmer_size" argument="-k" value="21" min="1" max="32" label="kmer size" />
2
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75 <param type="float" name="prob_threshold" argument="-w" value="0.01" min="0" max="1" label="Probability threshold for warning about low k-mer size" />
0
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76 </inputs>
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77 <outputs>
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78 <data name="sketch" format="msh" from_work_dir="sketch.msh"/>
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79 </outputs>
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80 <tests>
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81 <test>
2
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82 <conditional name="reads_assembly">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
83 <param name="reads_assembly_selector" value="reads"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
84 <conditional name="reads_input">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
85 <param name="reads_input_selector" value="single"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
86 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
87 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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88 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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89 <output name="sketch" file="test_01_mash_sketch.msh" compare="sim_size" />
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
90 </test>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
91 <test>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
92 <conditional name="reads_assembly">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
93 <param name="reads_assembly_selector" value="reads"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
94 <conditional name="reads_input">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
95 <param name="reads_input_selector" value="single"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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96 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
97 <param name="minimum_kmer_copies" value="10"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
98 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
99 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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100 <output name="sketch" file="test_02_mash_sketch.msh" compare="sim_size" />
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
101 </test>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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102 <test>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
103 <conditional name="reads_assembly">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
104 <param name="reads_assembly_selector" value="reads"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
105 <conditional name="reads_input">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
106 <param name="reads_input_selector" value="single"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
107 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
108 <param name="target_coverage" value="1"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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109 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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110 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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111 <output name="sketch" file="test_03_mash_sketch.msh" compare="sim_size" />
0
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
iuc
parents:
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112 </test>
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
iuc
parents:
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113 <test>
2
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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114 <conditional name="reads_assembly">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
115 <param name="reads_assembly_selector" value="reads"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
116 <conditional name="reads_input">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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117 <param name="reads_input_selector" value="single"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
118 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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119 <param name="genome_size" value="1000"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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120 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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121 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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122 <output name="sketch" file="test_04_mash_sketch.msh" compare="sim_size" />
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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123 </test>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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124 <test>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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125 <conditional name="reads_assembly">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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126 <param name="reads_assembly_selector" value="reads"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
127 <conditional name="reads_input">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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128 <param name="reads_input_selector" value="single"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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129 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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130 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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131 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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132 <param name="sketch_size" value="500"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
133 <output name="sketch" file="test_05_mash_sketch.msh" compare="sim_size" />
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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134 </test>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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135 <test>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
136 <conditional name="reads_assembly">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
137 <param name="reads_assembly_selector" value="reads"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
138 <conditional name="reads_input">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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139 <param name="reads_input_selector" value="single"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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140 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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141 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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142 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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143 <param name="kmer_size" value="17"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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144 <output name="sketch" file="test_06_mash_sketch.msh" compare="sim_size" />
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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145 </test>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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146 <test>
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iuc
parents: 0
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147 <conditional name="reads_assembly">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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148 <param name="reads_assembly_selector" value="reads"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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149 <conditional name="reads_input">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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150 <param name="reads_input_selector" value="single"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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151 <param name="reads" value="ERR024951_seqtk_sample_1000_1.fastq"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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152 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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153 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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154 <param name="prob_threshold" value="0.1"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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155 <output name="sketch" file="test_06_mash_sketch.msh" compare="sim_size" />
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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156 </test>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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157 <test>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
158 <conditional name="reads_assembly">
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
diff changeset
159 <param name="reads_assembly_selector" value="assembly"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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160 <param name="assembly" value="test_assembly.fasta"/>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
iuc
parents: 0
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161 </conditional>
91ee99b4f05a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 57309b08e7a08b6f72982f0d78cb5574616c7b67"
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parents: 0
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162 <output name="sketch" file="test_07_mash_sketch.msh" compare="sim_size" />
0
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
iuc
parents:
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163 </test>
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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parents:
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164 </tests>
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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parents:
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165 <help><![CDATA[
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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parents:
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166
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
iuc
parents:
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167 **What it does**
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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168
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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parents:
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169 Create a sketch file, which is a reduced representation of a sequence or set
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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170 of sequences (based on min-hashes) that can be used for fast distance
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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171 estimations. Inputs can be fasta or fastq files (gzipped or not), and "-" can
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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172 be given to read from standard input. Input files can also be files of file
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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173 names (see -l). For output, one sketch file will be generated, but it can have
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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174 multiple sketches within it, divided by sequences or files (see -i). By
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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175 default, the output file name will be the first input file with a '.msh'
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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176 extension, or 'stdin.msh' if standard input is used (see -o).
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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177 ]]></help>
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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178 <expand macro="citations"/>
68084b06ae83 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mash commit 24f4271bd62a3d96fec812eae2ad607f6a7f723c"
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179 </tool>