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annotate symlink_files.xml @ 0:909a7e8e9b30 draft

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planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
author mvdbeek
date Tue, 29 Nov 2016 10:03:30 -0500
parents
children 46dc0dbd9f04
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909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
mvdbeek
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1 <tool id="symlink_files" name="Symlink Files" version="0.1.3">
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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2 <requirements>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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3 </requirements>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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4 <stdio>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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5 <exit_code range="1:" />
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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6 </stdio>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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7 <command><![CDATA[
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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8 #if $__user_email__ not in $__admin_users__:
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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9 exit 1
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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10 #end if
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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11
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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12 #if $input:
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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13 mkdir -p '$output_path' &&
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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14 #if '$input.ext':
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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15 ln -fs '$input' '$output_path'/'$input.element_identifier'.'$input.ext'
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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16 #else:
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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17 ln -fs '$input' '$output_path'/'$input.element_identifier'
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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18 #end if
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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19 #end if
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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20 #if $input_collection:
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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21 mkdir -p '$output_path'/'$input_collection.name' &&
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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22 #for $element in $input_collection:
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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23 ln -fs '$element' '$output_path'/'$input_collection.name'/'$element.element_identifier'.'$element.ext';
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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24 #end for
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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25 #end if
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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26 #if $input_collection_paired:
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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27 mkdir -p '$output_path'/'$input_collection_paired.name' &&
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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28 #for $element in $input_collection_paired:
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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29 ln -fs '$element.forward' '$output_path'/'$input_collection_paired.name'/'$element.element_identifier'-forward.'$element.ext';
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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30 ln -fs '$element.reverse' '$output_path'/'$input_collection_paired.name'/'$element.element_identifier'-reverse.'$element.ext';
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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31 #end for
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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32 #end if
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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33 #if $input_collection_list_paired:
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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34 #for $sample in $input_collection_list_paired:
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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35 mkdir -p '$output_path'/'$input_collection_list_paired.name' &&
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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36 #for $element in $sample:
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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37 ln -fs '$element' '$output_path'/'$input_collection_list_paired.name'/'$sample.name'-$element.element_identifier.'$element.ext';
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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38 #end for
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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39 #end for
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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40 #end if
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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41 ]]></command>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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42 <inputs>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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43 <param name="input" optional="true" type="data" help="The file you would like to export"/>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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44 <param name="input_collection" optional="true" type="data_collection" collection_type="list" help="The collection you would like to export"/>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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45 <param name="input_collection_paired" optional="true" type="data_collection" collection_type="paired" help="The collection you would like to export"/>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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46 <param name="input_collection_list_paired" optional="true" type="data_collection" collection_type="list:paired" help="The collection you would like to export"/>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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47 <param name="output_path" type="text" help="Path to export to"/>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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48 </inputs>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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49 <outputs>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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50 </outputs>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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51 <help><![CDATA[
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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52 Creates symlinks to specified path.
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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53 ]]></help>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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54 </tool>