Mercurial > repos > rhpvorderman > data_manager_select_index_by_path
annotate data_manager/data_manager_select_index_by_path.xml @ 0:5f8d9309058b draft
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
author | rhpvorderman |
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date | Mon, 25 Sep 2017 03:35:26 -0400 |
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children | 8495c49cd056 |
rev | line source |
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5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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1 <tool id="data_manager_select_index_by_path" name="Select index by path manager" tool_type="manage_data" version="0.0.2"> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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2 <description>path inputer</description> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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3 <command interpreter="python"> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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4 path_name_value_key_manager.py |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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5 --value "${value}" |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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6 --dbkey "${dbkey}" |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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7 --name "${name}" |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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8 --path "${path}" |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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9 --data_table_name "${data_table}" |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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10 --json_output_file "${json_output_file}" |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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11 </command> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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12 <inputs> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff
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13 <param name="value" type="text" value="" label="value field for the entry. Defaults to name if left blank." /> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff
changeset
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14 <param name="dbkey" type="text" value="" label="dbkey field for the entry. Defaults to value if left blank." /> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff
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15 <param name="name" type="text" value="" label="name field for the entry. Defaults to the file name from path if left blank." /> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff
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16 <param name="path" type="text" value="" label="path field for the entry" /> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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17 <param name="data_table" type="select" value="" label="data table for the index"> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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18 <option value='all_fasta'>all_fasta</option> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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19 <option value='bowtie2_indexes'>bowtie2_indexes</option> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff
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20 <option value='bowtie_indexes'>bowtie_indexes</option> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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21 <option value='bowtie_indexes_color'>bowtie_indexes_color</option> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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22 <option value='bwa_mem_indexes'>bwa_mem_indexes</option> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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23 <option value='bwameth_indexes'>bwameth_indexes</option> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff
changeset
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24 <option value='fasta_indexes'>fasta_indexes</option> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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25 <option value='gatk_picard_indexes'>gatk_picard_indexes</option> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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26 <option value='gene_transfer'>gene_transfer</option> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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27 <option value='hisat2_indexes'>hisat2_indexes</option> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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28 <option value='kallisto_indexes'>kallisto_indexes</option> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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29 <option value='picard_indexes'>picard_indexes</option> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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30 <option value='tophat2_indexes'>tophat2_indexes</option> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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31 </param> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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32 </inputs> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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33 <outputs> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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34 <data name="json_output_file" format="data_manager_json"/> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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35 </outputs> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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36 |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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37 <help> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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38 Adds a server path to the selected data table. |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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39 |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
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40 The tool will check the path exists but NOT check that it holds the expected data type. |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
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41 |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
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42 If name is not provided the filename from path less the extension is used. |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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43 |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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44 If value is not provided, the name will be used (or its default) |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
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45 |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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46 If dbkey is not provided, the value will be used (or its default) |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
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47 |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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48 </help> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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49 <citations> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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50 </citations> |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
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51 |
5f8d9309058b
planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
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52 </tool> |