Mercurial > repos > iuc > data_manager_kallisto_index_builder
annotate data_manager/kallisto_index_builder.xml @ 0:6843a0db2da0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author | iuc |
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date | Sat, 05 Aug 2017 04:02:01 -0400 |
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children | 15c2fc266540 |
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6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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1 <tool id="kallisto_index_builder_data_manager" name="Kallisto" tool_type="manage_data" version="0.43.1"> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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2 <description>index builder</description> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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3 <requirements> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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4 <requirement type="package" version="0.43.1">kallisto</requirement> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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5 </requirements> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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6 <command detect_errors="exit_code"><![CDATA[ |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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7 python '$__tool_directory__/kallisto_index_builder.py' --output '${out_file}' |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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8 --fasta_filename '${all_fasta_source.fields.path}' |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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9 --fasta_dbkey '${all_fasta_source.fields.dbkey}' |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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10 --fasta_description '${all_fasta_source.fields.name}' |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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11 --data_table_name kallisto_indexes |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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12 ]]> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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13 </command> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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14 <inputs> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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15 <param label="Source FASTA Sequence" name="all_fasta_source" type="select"> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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16 <options from_data_table="all_fasta" /> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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17 </param> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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18 <param name="sequence_name" type="text" value="" label="Name of sequence" /> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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19 <param name="sequence_id" type="text" value="" label="ID for sequence" /> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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20 </inputs> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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21 <outputs> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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22 <data name="out_file" format="data_manager_json" /> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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23 </outputs> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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24 <help> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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25 <![CDATA[ |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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26 .. class:: infomark |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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27 |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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28 **Notice:** If you leave name, description, or id blank, it will be generated automatically. |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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29 |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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30 What is Kallisto? |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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31 --------------- |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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32 |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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33 `kallisto <https://pachterlab.github.io/kallisto/about>`__ is a program for |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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34 quantifying abundances of transcripts from RNA-Seq data, or more generally of |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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35 target sequences using high-throughput sequencing reads. It is based on the |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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36 novel idea of pseudoalignment for rapidly determining the compatibility of |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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37 reads with targets, without the need for alignment. On benchmarks with standard |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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38 RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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39 minutes on a Mac desktop computer using only the read sequences and a |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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40 transcriptome index that itself takes less than 10 minutes to build. |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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41 Pseudoalignment of reads preserves the key information needed for |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
iuc
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42 quantification, and kallisto is therefore not only fast, but also as accurate |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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43 as existing quantification tools. In fact, because the pseudoalignment |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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44 procedure is robust to errors in the reads, in many benchmarks kallisto |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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45 significantly outperforms existing tools. |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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46 ]]> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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47 </help> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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48 <citations> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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49 <citation type="doi">10.1038/nmeth.3317</citation> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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50 </citations> |
6843a0db2da0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_kallisto_index_builder commit 3b54163c4f7daff76fcc589c4a9057bb03904380
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51 </tool> |