Mercurial > repos > iuc > coverm_contig

annotate macros.xml @ 0:6941d0d453ba draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
author iuc
date Tue, 26 Apr 2022 15:27:37 +0000
parents
children 688a777e1b19
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6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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1 <macros>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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2 <xml name="requirements">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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3 <requirements>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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4 <requirement type="package">coverm</requirement>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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5 </requirements>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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6 </xml>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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7 <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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8 <token name="@TOOL_VERSION@">0.2.1</token>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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9 <token name="@VERSION_SUFFIX@">0</token>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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10 <xml name="citation">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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11 <citations>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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12 <citation type="bibtex">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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13 @misc{githubCoverm,
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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14 author = {B J. Woodcroft},
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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15 year = {2021},
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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16 title = {CoverM},
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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17 publisher = {GitHub},
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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18 journal = {GitHub repository},
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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19 url = {https://github.com/wwood/CoverM}
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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20 }
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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21 </citation>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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22 </citations>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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23 </xml>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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24 <xml name="genome_opt">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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25 <conditional name="genome">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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26 <param name="ref_or_genome" type="select" label="Select if you want to specify additional genome files.">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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27 <option value="genomic">yes</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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28 <option value="none" selected="true">No (Only when BAM files are provided)</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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29 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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30 <when value="none">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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31 <param argument="--single-genome" type="boolean" truevalue="--single-genome" falsevalue="" checked="false" label="All contigs are from the same genome."/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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32 <param type="text" name="separator" optional="true" label="Character, that separates genome names from contig names in the reference file." >
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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33 <sanitizer>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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34 <valid initial="string.punctuation">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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35 </valid>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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36 </sanitizer>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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37 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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38 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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39 <when value="genomic">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
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40 <conditional name="genomic">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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41 <param type="select" label="Reference genome source" name="source">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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42 <option value="history" selected="true">History</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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43 <option value="builtin">Built-in</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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44 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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45 <when value="history">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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46 <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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47 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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48 <when value="builtin">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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49 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome(s)">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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50 <options from_data_table="all_fasta" />
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51 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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52 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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53 </conditional>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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54 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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55 </conditional>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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56 </xml>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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57 <xml name="genome">
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58 <conditional name="genome">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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59 <param name="ref_or_genome" type="select" label="Reference sequence mode" help="Select if you want to specify genome file(s) or a FASTA reference file or both. NOTE: If genomic FASTA files are specified, then reference is not needed as a reference FASTA file can be derived by concatenating input genomes. However, while not necessary, reference can be specified if an alternate reference sequence set is desired.">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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60 <option value="genomic" selected="true">Reference genome</option>
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61 <option value="reference">Contigs (e.g. concatenated genomes or metagenome assembly)</option>
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62 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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63 <when value="genomic">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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64 <conditional name="genomic">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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65 <param type="select" label="Reference genome source" name="source">
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66 <option value="history" selected="true">History</option>
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67 <option value="builtin">Built-in</option>
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68 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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69 <when value="history">
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70 <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" />
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71 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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72 <when value="builtin">
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73 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome(s)">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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74 <options from_data_table="all_fasta" />
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75 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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76 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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77 </conditional>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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78 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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79 <when value="reference">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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80 <param type="data" name="ref_source" multiple="true" label="Contigs file(s)" format="fasta" help="If multiple references FASTA files are provided and 'sharded' is specified, then reads will be mapped to references separately as sharded BAMs."/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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81 <conditional name="cond_single_genome">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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82 <param name="single_genome" type="select" label="All contigs are from a single genome">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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83 <option value="--single-genome">True</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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84 <option value="false">False</option>
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85 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
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86 <when value="--single-genome">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
87 <param type="data" name="genome_definition" format="tsv" optional="true" label="File containing newline-separated list of genome_name and contig, separated by tab, to define the genome of each contig." />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
88 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
89 <when value="false">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
90 <param type="text" argument="--separator" optional="true" label="Character, that separates genome names from contig names in the reference file." >
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
91 <sanitizer>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
92 <valid initial="string.punctuation">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
93 </valid>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
94 </sanitizer>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
95 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
96 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
97 </conditional>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
98 <conditional name="add_genome">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
99 <param name="add_genome" type="boolean" label="Add additional Genome Files"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
100 <when value="true">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
101 <conditional name="add_genomic">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
102 <param type="select" label="Reference genome source" name="source">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
103 <option value="history" selected="true">History</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
104 <option value="builtin">Built-in</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
105 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
106 <when value="history">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
107 <param type="data" name="fasta_history" multiple="true" label="Single FASTA file of contigs" format="fasta" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
108 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
109 <when value="builtin">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
110 <param type="select" name="fasta_builtin" multiple="true" label="Reference genome">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
111 <options from_data_table="all_fasta" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
112 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
113 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
114 </conditional>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
115 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
116 <when value="false">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
117 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
118 </conditional>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
119 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
120 </conditional>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
121 </xml>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
122 <xml name="reads_for_contig">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
123 <conditional name="reads">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
124 <param type="select" label="Read type" name="read_type">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
125 <option value="paired">Paired end</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
126 <option value="paired_collection" selected="true">Paired collection</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
127 <option value="single">Single ended</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
128 <option value="interleaved">Interleaved</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
129 <option value="bam">BAM file(s)</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
130 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
131 <when value="paired">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
132 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
133 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
134 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
135 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
136 <when value="paired_collection">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
137 <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
138 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
139 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
140 <when value="single">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
141 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Single Read" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
142 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
143 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
144 <when value="interleaved">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
145 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
146 <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
147 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
148 <when value="bam">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
149 <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" help="BAM file(s). These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n). When specified, no read mapping algorithm is undertaken."/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
150 <param type="data" name="ref_fasta_history" optional="true" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
151 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
152 </conditional>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
153 </xml>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
154 <xml name="reads">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
155 <conditional name="reads">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
156 <param type="select" label="Read type" name="read_type">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
157 <option value="single">Single ended</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
158 <option value="paired">Paired end</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
159 <option value="paired_collection" selected="true">Paired collection</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
160 <option value="interleaved">Interleaved</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
161 <option value="bam">BAM file(s)</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
162 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
163 <when value="paired">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
164 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
165 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
166 <expand macro="genome"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
167 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
168 <when value="paired_collection">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
169 <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="Collection of paired-reads" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
170 <expand macro="genome"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
171 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
172 <when value="single">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
173 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Single Read" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
174 <expand macro="genome"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
175 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
176 <when value="interleaved">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
177 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
178 <expand macro="genome"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
179 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
180 <when value="bam">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
181 <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" help="BAM file(s). These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n). When specified, no read mapping algorithm is undertaken."/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
182 <expand macro="genome_opt"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
183 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
184 </conditional>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
185 </xml>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
186 <xml name="add_reads">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
187 <section name="add_reads" title="Add an additional read">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
188 <conditional name="extra_read">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
189 <param type="select" label="Read type" optional="true" name="read_type">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
190 <option value="none" selected="true">None</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
191 <option value="paired">Paired end</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
192 <option value="paired_collection">Paired collection</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
193 <option value="single">Single ended</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
194 <option value="interleaved">Interleaved</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
195 <option value="bam">BAM file(s)</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
196 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
197 <when value="none">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
198 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
199 <when value="paired">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
200 <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
201 <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
202 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
203 <when value="paired_collection">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
204 <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
205 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
206 <when value="single">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
207 <param type="data" format="@INPUT_FORMATS@" name="single" multiple="true" label="Single read" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
208 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
209 <when value="interleaved">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
210 <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
211 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
212 <when value="bam">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
213 <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
214 </when>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
215 </conditional>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
216 </section>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
217 </xml>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
218 <xml name="mapping">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
219 <section name="mapping" title="Mapping options" expanded="false">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
220 <param argument="--mapper" optional="true" type="select" label="Mapper" help="Underlying mapping software used. Default: minimap2-sr" >
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
221 <option value="minimap2-sr">minimap2 with '-x sr' option</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
222 <option value="minimap2-ont">minimap2 with '-x map-ont' option</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
223 <option value="minimap2-pb">minimap2 with '-x map-pb' option</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
224 <option value="minimap2-no-preset">minimap2 with no '-x' option</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
225 <option value="bwa-mem">BWA-MEM using default parameters</option>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
226 </param>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
227 <param argument="--min_read-aligned-length" type="integer" min="0" value="0"
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
228 label="Min read aligned length" help="Exclude reads with smaller numbers of aligned bases. Default: 0" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
229 <param argument="--min_read-percent-identity" type="float" min="0" max="100" value="0"
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
230 label="Min read percent identity" help="Exclude reads by overall percent identity e.g. 95 for 95%. Default: 0" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
231 <param argument="--min_read-aligned-percent" type="float" min="0" max="100" value="0"
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
232 label="Min read aligned percentage" help="Exclude reads by percent aligned bases e.g. 95 means 95%
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
233 of the read's bases must be aligned. Default: 0" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
234 <param argument="--min_read-aligned-length-pair" type="integer" min="0" value="0"
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
235 label="Min read aligned length pair" help="Exclude pairs with smaller numbers of aligned bases.
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
236 Implies --proper-pairs-only. Default: 0" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
237 <param argument="--min_read-percent-identity-pair" type="float" min="0" max="100" value="0"
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
238 label="Min read percent identity pair" help="Exclude pairs by overall percent identity e.g. 95 for 95%.
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
239 Implies --proper-pairs-only. Default: 0" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
240 <param argument="--min_read-aligned-percent-pair" type="float" min="0" max="100" value="0"
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
241 label="Min read aligned percentage pair" help="Exclude reads by percent aligned bases e.g. 95 means 95% of
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
242 the read's bases must be aligned. Implies --proper-pairs-only. Default: 0" />
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
243 <param argument="--proper-pairs-only" type="boolean" truevalue="--proper-pairs-only" falsevalue=""
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
244 label="Require reads to be mapped as proper pairs" help="Default: not set"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
245 <param argument="--exclude-supplementary" type="boolean" truevalue="--exclude-supplementary" falsevalue=""
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
246 label="Exclude supplementary alignments" help="Default: not set"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
247 </section>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
248 </xml>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
249 <xml name="coverage">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
250 <section name="cov" title="Coverage calculation options" expanded="false">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
251 <param name="relative_abundance" type="boolean" falsevalue="" truevalue="relative_abundance" label="Relative abundance (default)"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
252 <param name="mean" type="boolean" falsevalue="" truevalue="mean" label="Mean"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
253 <conditional name="cond_methods">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
254 <param name="trimmed_mean" type="boolean" falsevalue="" truevalue="trimmed_mean" label="Trimmed mean"/>
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
diff changeset
255 <when value="trimmed_mean">
6941d0d453ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 5a4ee5e5f8eee3a08a1cd2dfd9edf15aacea0a94"
iuc
parents:
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256 <param name="trim_min" type="integer" min="0" value="5" label="Trim min" help="Remove this smallest fraction of positions when calculating trimmed_mean default: 5"/>
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257 <param name="trim_max" type="integer" min="0" value="95" label="Trim max" help="Maximum fraction for trimmed_mean calculations default: 95"/>
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258 </when>
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259 <when value=""/>
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260 </conditional>
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261 <param name="covered_bases" type="boolean" falsevalue="" truevalue="covered_bases" label="Covered bases"/>
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262 <param name="covered_fraction" type="boolean" falsevalue="" truevalue="covered_fraction" label="Covered fraction"/>
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263 <param name="variance" type="boolean" falsevalue="" truevalue="variance" label="Variance"/>
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264 <param name="length" type="boolean" falsevalue="" truevalue="length" label="Length"/>
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265 <param name="count" type="boolean" falsevalue="" truevalue="count" label="Count"/>
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266 <param name="metabat" type="boolean" falsevalue="" truevalue="metabat" label="MetaBAT"/>
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267 <param name="coverage_histogram" type="boolean" falsevalue="" truevalue="coverage_histogram" label="Coverage histogram"/>
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268 <param name="reads_per_base" type="boolean" falsevalue="" truevalue="reads_per_base" label="Reads per base"/>
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269 <param name="rpkm" type="boolean" falsevalue="" truevalue="rpkm" label="RPKM"/>
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270 <param name="tpm" type="boolean" falsevalue="" truevalue="tpm" label="TPKM"/>
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271 <param name="min_covered_fraction" type="integer" min="0" optional="true"
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272 label="Min covered fraction" help="Genomes with less coverage than this reported as having zero coverage. Default: 10"/>
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273 <param name="contig_end_exclusion" type="integer" min="0" optional="true"
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274 label="Contig end exclusion" help="Exclude bases at the ends of reference sequences from calculation. Default: 75"/>
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275 </section>
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276 </xml>
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277 <xml name="out">
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278 <section name="out" title="Output options" expanded="false">
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279 <param name="output_format" type="select" label="Shape of output" help="'Sparse' for long format, 'dense' for species-by-site. Default: dense]">
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280 <option value="dense" selected="true">Dense</option>
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281 <option value="sparse">Sparse</option>
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282 </param>
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283 <param name="no_zeros" type="boolean" truevalue="--no-zeros" falsevalue="" optional="true" label="Omit printing of genomes that have zero coverage" />
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284 <param argument="--dereplication-output-cluster-definition" type="boolean" truevalue="--dereplication-output-cluster-definition" falsevalue="" label="Output a file of representative TAB member lines." />
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285 <param argument="--dereplication-output-representative-fasta-directory-copy" type="boolean" truevalue="--dereplication-output-representative-fasta-directory-copy" falsevalue="" label="Output representative genomes" />
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286 </section>
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287 </xml>
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288 <xml name="citations">
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289 <citations>
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290 <yield />
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291 </citations>
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292 </xml>
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293 </macros>