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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
author bgruening
date Thu, 09 Mar 2017 08:31:45 -0500
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d0bfaeca5e25 planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
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1 <tool id="hicup_digester" name="Hicup Digester" version="0.1.0">
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2 <description>cuts throughout a selected genome at one or two specified restriction sites.</description>
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3 <macros>
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4 <import>hicup_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements_hicup" />
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7 <expand macro="stdio" />
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8
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9 <command><![CDATA[
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10 hicup_digester --re1 '$re1' --genome '$genome'
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11 #if $advanced_options.re2:
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12 --re2 '$advanced_options.re2'
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13 #end if
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14 #for $file in $input_files_digest:
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15 $file
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16 #end for
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17 && mv *Digest_* digester_file.txt
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18 ]]></command>
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19 <inputs>
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20 <expand macro="digester_input" />
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21 <expand macro="re1" />
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22 <section name="advanced_options" title="Advanced options">
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23 <expand macro="re2" />
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24 </section>
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25 </inputs>
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26 <outputs>
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27 <data name="digest_file" format="txt" from_work_dir="digester_file.txt" label="Digester File.txt"/>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="input_files_digest" value="chr1.fa"/>
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32 <param name="re1" value="A^AGCTT"/>
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33 <param name="genome" value="human"/>
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34 <output name="digest_file" file="digester_file.txt" lines_diff="4"/>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38
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39 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
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40
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41 To get more information about the digister visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Digester
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42 ]]></help>
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43 <expand macro="citation_hicup" />
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44 </tool>