Mercurial > repos > bgruening > strip_it

annotate strip-it.xml @ 0:fc8d71a0fb9b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
author bgruening
date Mon, 22 May 2017 03:01:21 -0400
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0
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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1 <tool id="ctb_stripit" name="Strip-it" version="1.0.2.1">
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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2 <description>extracts predefined scaffolds from molecules</description>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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3 <!--parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" shared_inputs="" merge_outputs="outfile"></parallelism-->
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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4 <requirements>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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5 <requirement type="package" version="1.0.2">strip_it</requirement>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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6 </requirements>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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7 <command detect_errors="aggressive">
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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8 <![CDATA[
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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9 ln -s '$infile' '$infile.${infile.ext}' &&
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
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10 strip-it
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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11 --input '$infile.${infile.ext}'
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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12 --output '$outfile'
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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13 --noLog
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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14 $noHeader
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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15 ]]>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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16 </command>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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17 <inputs>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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18 <param name="infile" type="data" format='sdf,mol,mol2,smi' label="Molecule file" />
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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19 <param argument='--noHeader' type='boolean' truevalue='--noHeader' falsevalue=''
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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20 label='Do not print a header in the output file' />
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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21
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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22 </inputs>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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23 <outputs>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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24 <data name="outfile" format="tabular" />
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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25 </outputs>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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26 <tests>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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27 <test>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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28 <param name="infile" ftype="sdf" value="CID_3037.sdf"/>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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29 <param name="noHeader" value="false"/>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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30 <output name="outfile" file="Strip-it_on_CID3037.tabular" />
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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31 </test>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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32 </tests>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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33 <help>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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34 <![CDATA[
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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35
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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37 .. class:: infomark
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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38
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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39 **What this tool does**
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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40
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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41 Strip-it is a program that extracts predefined scaffolds from organic small
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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42 molecules.
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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43
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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44 The program comes with a number of predefined molecular scaffolds for
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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45 extraction. These scaffolds include, amongst others
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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46
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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47 - `molecular frameworks`_ as originally described by Bemis and Murcko
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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48 - `molecular frameworks and the reduced molecular frameworks`_ as described by Ansgar Schuffenhauer and coworkers
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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49 - `scaffold topologies`_ as described by Sara Pollock and coworkers
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50
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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51 .. _molecular frameworks: http://www.ncbi.nlm.nih.gov/pubmed/8709122
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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52 .. _molecular frameworks and the reduced molecular frameworks: http://peter-ertl.com/reprints/Schuffenhauer-JCIM-47-47-2007.pdf
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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53 .. _scaffold topologies: http://www.ncbi.nlm.nih.gov/pubmed/18605680
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55 -----
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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57 .. class:: infomark
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fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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60 **Input**
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fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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62 | - `SD-Format`_
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63 | - `SMILES Format`_
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64 | - `MOL2 Format`_
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66 .. _SD-Format: http://en.wikipedia.org/wiki/Chemical_table_file
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67 .. _SMILES Format: http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification
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68 .. _MOL2 Format: http://chemyang.ccnu.edu.cn/ccb/server/AIMMS/mol2.pdf
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71 -----
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73 .. class:: infomark
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75 **Output**
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77 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
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78 | NAME | MOLECULE | RINGS_WITH_LINKERS_1 | RINGS_WITH_LINKERS_2 | MURCKO_1 | ... |
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
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79 +=============+================================+======================+========================+======================+=====+
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
80 | Diclofenac | OC(=O)Cc1ccccc1Nc1c(Cl)cccc1Cl | c1ccc(cc1)Nc1ccccc1 | c1ccc(cc1)Nc1ccccc1 | C1CCC(CC1)CC1CCCCC1 | ... |
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
81 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
82 | Bupivacaine | CCCCN1CCCCC1C(=O)Nc1c(C)cccc1C | C1CCC(NC1)CNc1ccccc1 | O=C(C1CCCCN1)Nc1ccccc1 | C1CCC(CC1)CCC1CCCCC1 | ... |
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
83 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
84 | ... | ... | ... | ... | ... | ... |
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
85 +-------------+--------------------------------+----------------------+------------------------+----------------------+-----+
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
86
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
87 -----
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
88
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
89 .. class:: infomark
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
90
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
91 **Cite**
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
92
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
93 `Silicos-it`_ - strip-it
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
94
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
95 .. _Silicos-it: http://silicos-it.be.s3-website-eu-west-1.amazonaws.com/software/strip-it/1.0.2/strip-it.html
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
96
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
97
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
98 ]]>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
99 </help>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
100 <citations>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
101 </citations>
fc8d71a0fb9b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/silicos-it/strip-it commit c30f4f5b484d97e8a12d0cb968abeeeafca750d7
bgruening
parents:
diff changeset
102 </tool>