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1 <?xml version="1.0"?>
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2
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3 <tool name="Upload File" id="cadds_upload" version="1.1.2">
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4 <description>
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5 from your computer
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6 </description>
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7 <action module="galaxy.tools.actions.upload" class="UploadToolAction"/>
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8 <command interpreter="python">
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9 ../../../data_source/upload.py $GALAXY_ROOT_DIR $GALAXY_DATATYPES_CONF_FILE $paramfile
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10 #set $outnum = 0
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11 #while $varExists('output%i' % $outnum):
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12 #set $output = $getVar('output%i' % $outnum)
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13 #set $outnum += 1
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14 ${output.dataset.dataset.id}:${output.files_path}:${output}
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15 #end while
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16 </command>
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17 <inputs nginx_upload="true">
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18 <param name="file_type" type="select" label="File Format" help="Which format? See help below">
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19 <options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ "%s%s%s" % ( line, self.separator, line ) for line in obj ]">
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20 <column name="value" index="1"/>
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21 <column name="name" index="0"/>
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22 <filter type="sort_by" column="0"/>
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23 <filter type="add_value" name="Auto-detect" value="auto" index="0"/>
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24 </options>
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25 </param>
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26 <param name="async_datasets" type="hidden" value="None"/>
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27 <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type" metadata_ref="files_metadata">
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28 <param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: For NGS and other large files (>~2GB), uploading via HTTP/FTP URL (below) is the most reliable method.">
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29 <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator> <!-- use validator to post message to user about needing to reselect the file, since most browsers won't accept the value attribute for file inputs -->
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30 </param>
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31 <param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/>
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32 <param name="ftp_files" type="ftpfile" label="Files uploaded via FTP"/>
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33 <!--
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34 <param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand.">
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35 <option value="Yes">Yes</option>
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36 </param>
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37 -->
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38 </upload_dataset>
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39 <!--<param name="dbkey" type="genomebuild" label="Genome" />-->
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40 <conditional name="files_metadata" title="Specify metadata" value_from="self:app.datatypes_registry.get_upload_metadata_params" value_ref="file_type" value_ref_in_group="False" />
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41 <!-- <param name="other_dbkey" type="text" label="Or user-defined Genome" /> -->
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42 </inputs>
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43 <help>
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44
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45 </help>
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46 </tool>
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