Mercurial > repos > jjohnson > split_to_collection

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
author jjohnson
date Thu, 26 Oct 2017 13:32:38 -0400
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f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
jjohnson
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1 <tool id="split_tabular_to_collection" name="Split Tabular into Collection" version="0.1.0">
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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2 <description>by lines</description>
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3 <command><![CDATA[
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4 #set $width = len(str($input.dataset.metadata.data_lines))
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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5 #if $skip_comment_lines:
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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6 #set $skip = $input.dataset.metadata.comment_lines
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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7 #else
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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8 #set $skip = 0
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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9 #end if
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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10 #set $offset = $skip + 1
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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11 awk 'NR > $skip{ print \$0 > (sprintf("%s_%.${width}d","${input.name}",int((NR-${offset})/${lines})*${lines}) ) }' $input
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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12 ]]></command>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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13 <inputs>
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14 <param name="input" type="data" format="tabular" label="Tabular dataset to split"/>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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15 <param name="lines" type="integer" value="1000" min="1" label="Number of lines per output dataset"/>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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16 <param name="skip_comment_lines" type="boolean" truevalue="yes" falsevalue="no" checked="true"
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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17 label="Skip comment lines"/>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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18 </inputs>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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19 <outputs>
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20 <collection name="output_set" type="list" label="${input.name} Split List">
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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21 <discover_datasets pattern="__name__" ext="tabular" visible="false"/>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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22 </collection>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="input" value="input.tsv" ftype="tabular"/>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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27 <param name="lines" value="20"/>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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28 <output_collection name="output_set" type="list">
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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29 <element name="input.tsv_00">
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30 <assert_contents>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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31 <has_text_matching expression="20\tt\tT" />
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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32 </assert_contents>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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33 </element>
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34 <element name="input.tsv_00">
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35 <assert_contents>
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36 <has_text_matching expression="21\tu\tU" />
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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37 </assert_contents>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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38 </element>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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39 </output_collection>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 Splits a tabular dataset into multiple datsets in a dataset collection.
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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44 This can be used in a workflow to process datasets in the collection in parallel.
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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45
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46 ]]></help>
f6254e4e155e planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/split_to_collection commit b2ce04dd96d8b00103c23b58a4c6539a6b30809a-dirty
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47 </tool>