Mercurial > repos > iuc > kallisto_quant

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f173f58bc695c22364685c2ffbb9f3e95708f00f
author iuc
date Mon, 05 Jun 2023 22:05:32 +0000
parents 8bb5d2582782
children
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16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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1 <?xml version="1.0"?>
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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2 <macros>
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3 <token name="@TOOL_VERSION@">0.48.0</token>
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81c9f0ba13d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f173f58bc695c22364685c2ffbb9f3e95708f00f
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4 <token name="@VERSION_SUFFIX@">1</token>
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16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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5 <xml name="requirements">
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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6 <requirements>
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90e937ec7df8 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit c657f8cc0308cd70b26e3b111e5d8008901cda24"
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7 <requirement type="package" version="@TOOL_VERSION@">kallisto</requirement>
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8bb5d2582782 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 168993a4e148506b1d3998c536caa2e501c36ccf
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8 <requirement type="package" version="1.14">samtools</requirement>
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16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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9 </requirements>
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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10 </xml>
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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11 <xml name="citations">
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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12 <citations>
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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13 <citation type="doi">doi:10.1038/nbt.3519</citation>
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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14 </citations>
16c923816e87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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15 </xml>
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16 <xml name="reference_input">
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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17 <conditional name="reference_transcriptome">
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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18 <param name="reference_transcriptome_source" type="select" label="Reference transcriptome for quantification">
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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19 <option value="indexed" selected="true">Use a built-in transcriptome</option>
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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20 <option value="history">Use a transcriptome from history</option>
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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21 </param>
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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22 <when value="indexed">
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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23 <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy administrator">
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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24 <options from_data_table="kallisto_indexes">
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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25 <filter type="sort_by" column="2" />
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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26 <validator type="no_options" message="No transcriptomes are available for the selected input dataset" />
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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27 </options>
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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28 </param>
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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29 </when>
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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30 <when value="history">
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31 <param name="reference" type="data" format="fasta" label="FASTA reference transcriptome" />
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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32 </when>
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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33 </conditional>
22c498dc4bc6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit 011de86c970114d5ae22f76e9ee8e2d86c190063
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34 </xml>
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35 <xml name="macro_lib_type">
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36 <param name="lib_type" type="select" label="Library strandness information">
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37 <option value="">Unstranded</option>
81c9f0ba13d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f173f58bc695c22364685c2ffbb9f3e95708f00f
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38 <option value="--fr-stranded">Strand specific reads, first read forward</option>
81c9f0ba13d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f173f58bc695c22364685c2ffbb9f3e95708f00f
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39 <option value="--rf-stranded">Strand specific reads, first read reverse</option>
81c9f0ba13d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f173f58bc695c22364685c2ffbb9f3e95708f00f
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40 </param>
81c9f0ba13d2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/kallisto/ commit f173f58bc695c22364685c2ffbb9f3e95708f00f
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41 </xml>
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42 </macros>