Mercurial > repos > iuc > data_manager_salmon_index_builder

annotate data_manager/salmon_index_builder.xml @ 0:9ab615bea004 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
author iuc
date Wed, 24 Jul 2019 07:16:36 -0400
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children d6fae6adc2b1
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9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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1 <tool id="salmon_index_builder_data_manager" name="Salmon" tool_type="manage_data" version="0.11.3" profile_version="19.01">
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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2 <description>index builder</description>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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3 <requirements>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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4 <requirement type="package" version="0.11.3">salmon</requirement>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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5 <requirement type="package" version="3.7">python</requirement>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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6 </requirements>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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7 <macros>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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8 <token name="@IDX_VERSION@">q5</token>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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9 </macros>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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10 <command detect_errors="exit_code"><![CDATA[
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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11 python '$__tool_directory__/salmon_index_builder.py' --output '${out_file}'
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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12 --fasta_filename '${all_fasta_source.fields.path}'
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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13 --fasta_dbkey '${all_fasta_source.fields.dbkey}'
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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14 --fasta_description '${all_fasta_source.fields.name}'
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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15 --kmer_size "${kmer_size}"
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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16 --data_table_name salmon_indexes_versioned
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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17 --index_version @IDX_VERSION@
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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18 ]]>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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19 </command>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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20 <inputs>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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21 <param label="Source FASTA Sequence" name="all_fasta_source" type="select">
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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22 <options from_data_table="all_fasta" />
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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23 </param>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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24 <param name="sequence_name" type="text" value="" label="Name of sequence" />
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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25 <param name="sequence_id" type="text" value="" label="ID for sequence" />
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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26 <param name="kmer_size" type="integer" optional='true' value="21" max="32" label="The size of the k-mer on which the index is built"
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
iuc
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27 help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors. The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers, the more distinct they will be. We generally recommend using a k-mer size of at least 20. MUST BE AN ODD VALUE "/>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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28 </inputs>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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29 <outputs>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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30 <data name="out_file" format="data_manager_json" />
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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31 </outputs>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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32 <tests>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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33 <test>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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34 <param name="all_fasta_source" value="phiX174"/>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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35 <param name="sequence_name" value="sequence_name"/>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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36 <param name="sequence_id" value="sequence_id"/>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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37 <output name="out_file" file="salmon_phiX174.data_manager_json"/>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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38 </test>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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39 </tests>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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40 <help>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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41 <![CDATA[
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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42 .. class:: infomark
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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43
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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44 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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45 ]]>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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46 </help>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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47 <citations>
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48 <citation type="doi">https://doi.org/10.1038/nmeth.4197</citation>
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49 </citations>
9ab615bea004 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_salmon_index_builder commit 473215c1fea036954d18a7ce339f914f7cf0655b
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50 </tool>