Mercurial > repos > iuc > meryl_histogram_kmers

annotate macros.xml @ 1:9b6d82198a62 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
author iuc
date Sun, 09 Nov 2025 18:35:46 +0000
parents 16b7b0d0eaea
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16b7b0d0eaea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit a3a16149db71f9b72dd7e949df0db08797637312
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1 <macros>
1
9b6d82198a62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
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2 <token name="@TOOL_VERSION@">1.4.1</token>
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3 <token name="@GALAXY_TOOL_VERSION@">galaxy</token>
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4 <token name="@SUFFIX_VERSION@">0</token>
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5 <token name="@PROFILE@">22.01</token>
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6 <xml name="edam_ontology">
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7 <edam_topics>
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8 <edam_topic>topic_0196</edam_topic>
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9 </edam_topics>
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10 <edam_operations>
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11 <edam_operation>operation_0525</edam_operation>
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12 </edam_operations>
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13 </xml>
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14 <xml name="requirements">
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15 <requirements>
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16 <requirement type="package" version="1.1">merqury</requirement>
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17 <requirement type="package" version="@TOOL_VERSION@">meryl</requirement>
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18 <requirement type="package" version="1.34">tar</requirement>
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19 <requirement type="package" version="2.8">pigz</requirement>
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20 </requirements>
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21 </xml>
1
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22 <xml name="kmer_param">
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23 <conditional name="options_kmer_size">
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24 <param name="kmer_size" type="select" label="K-mer size selector">
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25 <option value="provide">Set a k-mer size</option>
9b6d82198a62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
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26 <option value="estimate">Estimate the best k-mer size</option>
9b6d82198a62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
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27 </param>
9b6d82198a62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
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28 <when value="provide">
9b6d82198a62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
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29 <param name="input_kmer_size" type="integer" min="1" value="" label="K-mer size" help="For a human genome, the best k-mer size is k=21 for both haploid (3.1G) or diploid (6.2G).."/>
9b6d82198a62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
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30 </when>
9b6d82198a62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
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31 <when value="estimate">
9b6d82198a62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
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32 <param name="genome_size" type="integer" min="1000" max="70000000000" value="1000" label="Genome size" help="Haploid genome size or diploid genome size, depending on what we evaluate. In bp. Only required if the k-mer size is not provided."/>
9b6d82198a62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
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33 <param name="collision_rate" type="float" min="0.0001" max="0.01" value="0.001" label="Tolerable collision rate" help="Tolerable collision rate. By default is 0.001."/>
9b6d82198a62 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl commit 6935ad9dddbbb913817552d682d0b2208481dc7f
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34 </when>
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35 </conditional>
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36 </xml>
0
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37 <xml name="meryldb_archive_assumptions">
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38 <has_archive_member path="^[^/]+.meryl$" n="1"/> <!-- folder also counts -->
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39 <has_archive_member path="[^/]+.meryl/merylIndex" n="1" all="true">
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40 <has_size min="1"/>
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41 </has_archive_member>
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42 <has_archive_member path="[^/]+.meryl/.*\.merylIndex" n="64" all="true">
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43 <has_size min="1"/>
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44 </has_archive_member>
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45 <has_archive_member path="[^/]+.meryl/.*\.merylData" n="64" all="true">
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46 <!-- <has_size min="1"/> seems to be 0 sometimes -->
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47 </has_archive_member>
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48 <has_archive_member path=".*" n="130"/>
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49 </xml>
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50 <xml name="citations">
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51 <citations>
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52 <citation type="bibtex">
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53 @misc{githubMeryl,
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54 author = {Arang Rhie, Brian P. Walez, Sergey Koren, Adam M. Phillippy},
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55 year = {2020},
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56 title = {Meryl},
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57 publisher = {GitHub},
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58 journal = {GitHub repository},
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59 url = {https://github.com/marbl/meryl},
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60 }
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61 </citation>
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62 </citations>
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63 </xml>
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64 </macros>