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1 <tool id="load_reference_datasets" name="Load built-in reference data to history" version="0.0.1" >
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2 <command><![CDATA[
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3 #if $input_source.table_type_selector == "gff":
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4 out_name=\$(sed 's/ /_/g' <<< "$input_source.gff.fields.name");
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5 cp $input_source.gff.fields.path \$out_name.gff;
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6 #else:
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7 out_name=\$(sed 's/ /_/g' <<< "$input_source.fasta.fields.name");
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8 cp $input_source.fasta.fields.path \$out_name.fasta;
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9 #end if
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10 ]]></command>
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11 <inputs>
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12 <conditional name="input_source">
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13 <param name="table_type_selector" type="select" label="Select the type of file you want to access">
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14 <option value="gff" selected='True'>Annotations (GFF/GTF) files</option>
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15 <option value="fasta">FASTA Files (Genomes files / cDNA / etc)</option>
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16 </param>
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17 <when value="full">
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18 <param name="gff" type="select" label="Select the annotation file from the list" help="If your genome of interest is not listed contact the Galaxy admin">
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19 <options from_data_table="all_gff"/>
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20 </param>
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21 </when>
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22 <when value="fasta">
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23 <param name="fasta" type="select" label="Select the FASTA file from the list" help="if your genome of interest is not listed contact the Galaxy admin">
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24 <options from_data_table="all_fasta"/>
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25 </param>
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26
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27 </when>
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28 </conditional>
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29 </inputs>
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30 <outputs>
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31 <data name="copied_file" label="">
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32 <discover_datasets pattern="__designation_and_ext__" visible="true" />
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33 </data>
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34 </outputs>
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35 <help>
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36 **What it does**
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37
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38 This tool allows loading different built-in datasets into your history using the same data tables access that any other tool uses.
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39
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40
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41 </help>
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42 </tool>
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