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planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 71625ec1a2b288417d5e47d1e7252620e39c8611
author mvdbeek
date Tue, 29 Nov 2016 10:53:10 -0500
parents 46dc0dbd9f04
children
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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
mvdbeek
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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 '$input.ext':
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46dc0dbd9f04 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit b0ef7aecb1a8917fc220f376af211df14e8c68ba
mvdbeek
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15 #if input.ext == 'bam':
46dc0dbd9f04 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit b0ef7aecb1a8917fc220f376af211df14e8c68ba
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16 ln -fs '$input.metadata.bam_index' '$output_path'/'$input.element_identifier'.'$input.ext'.bai &&
46dc0dbd9f04 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit b0ef7aecb1a8917fc220f376af211df14e8c68ba
mvdbeek
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17 #end if
2
301f0997a1da planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 71625ec1a2b288417d5e47d1e7252620e39c8611
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18 ln -fs \$(readlink '$input') '$output_path'/'$input.element_identifier'.'$input.ext'
0
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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19 #else:
2
301f0997a1da planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 71625ec1a2b288417d5e47d1e7252620e39c8611
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20 ln -fs \$(readlink '$input') '$output_path'/'$input.element_identifier'
0
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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21 #end if
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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22 #end if
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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23 #if $input_collection:
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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24 mkdir -p '$output_path'/'$input_collection.name' &&
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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25 #for $element in $input_collection:
1
46dc0dbd9f04 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit b0ef7aecb1a8917fc220f376af211df14e8c68ba
mvdbeek
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26 #if $element.ext == 'bam':
46dc0dbd9f04 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit b0ef7aecb1a8917fc220f376af211df14e8c68ba
mvdbeek
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27 ln -fs '$element.metadata.bam_index' '$output_path'/'$input_collection.name'/'$element.element_identifier'.'$element.ext'.bai &&
46dc0dbd9f04 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit b0ef7aecb1a8917fc220f376af211df14e8c68ba
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28 #end if
2
301f0997a1da planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 71625ec1a2b288417d5e47d1e7252620e39c8611
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29 ln -fs \$(readlink '$element') '$output_path'/'$input_collection.name'/'$element.element_identifier'.'$element.ext';
0
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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30 #end for
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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31 #end if
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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32 #if $input_collection_paired:
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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33 mkdir -p '$output_path'/'$input_collection_paired.name' &&
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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34 #for $element in $input_collection_paired:
2
301f0997a1da planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 71625ec1a2b288417d5e47d1e7252620e39c8611
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35 ln -fs \$(readlink '$element.forward') '$output_path'/'$input_collection_paired.name'/'$element.element_identifier'-forward.'$element.ext';
301f0997a1da planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 71625ec1a2b288417d5e47d1e7252620e39c8611
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36 ln -fs \$(readlink '$element.reverse') '$output_path'/'$input_collection_paired.name'/'$element.element_identifier'-reverse.'$element.ext';
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909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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37 #end for
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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38 #end if
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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39 #if $input_collection_list_paired:
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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40 #for $sample in $input_collection_list_paired:
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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41 mkdir -p '$output_path'/'$input_collection_list_paired.name' &&
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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42 #for $element in $sample:
2
301f0997a1da planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 71625ec1a2b288417d5e47d1e7252620e39c8611
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43 ln -fs \$(readlink '$element') '$output_path'/'$input_collection_list_paired.name'/'$sample.name'-$element.element_identifier.'$element.ext';
0
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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44 #end for
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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45 #end for
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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46 #end if
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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47 ]]></command>
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 <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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50 <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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51 <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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52 <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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53 <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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54 </inputs>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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55 <outputs>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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56 </outputs>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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57 <help><![CDATA[
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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58 Creates symlinks to specified path.
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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59 ]]></help>
909a7e8e9b30 planemo upload for repository https://github.com/mvdbeek/gx_symlinks commit 979b3a88f038dbeddcc2c0a59c7b1ca2a181af75
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60 </tool>