Mercurial > repos > bgruening > hicup_hicup
annotate hicup_hicup.xml @ 4:bd1594d55a38 draft
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
author | bgruening |
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date | Fri, 25 May 2018 17:53:14 -0400 |
parents | e96cb39c3f8e |
children | 6137fb382a02 |
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e96cb39c3f8e
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit c546c919808a853d3e1556cb28bb4a5f7e1f9932
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1 <tool id="hicup_hicup" name="Hicup Pipeline" version="@VERSION@.0"> |
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7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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2 <description>controls the other programs in the HiCUP pipeline.</description> |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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3 <macros> |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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4 <import>hicup_macros.xml</import> |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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5 </macros> |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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6 <expand macro="requirements_hicup" /> |
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bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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7 |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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8 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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9 |
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bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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10 ##Dealing with fastq and fastq.gz |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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11 #if $input_first_sequence.is_of_type("fastq.gz", "fastqsanger.gz"): |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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12 ln -s $input_first_sequence dataset1.gz && |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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13 #set input1='dataset1.gz' |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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14 #else |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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15 ln -s $input_first_sequence dataset1 && |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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16 #set input1='dataset1' |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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17 #end if |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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18 |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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19 |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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20 #if $input_second_sequence.is_of_type("fastq.gz", "fastqsanger.gz"): |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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21 ln -s $input_second_sequence dataset2.gz && |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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22 #set input2='dataset2.gz' |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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23 #else |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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24 ln -s $input_second_sequence dataset2 && |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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25 #set input2='dataset2' |
bd1594d55a38
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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26 #end if |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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27 |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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28 BOWTIE_PATH_BASH="\$(which bowtie2)" && |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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29 #set index_path = '' |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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30 #if str($reference_genome.source) == "history": |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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31 bowtie2-build "$reference_genome.own_file" genome && |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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32 ln -s "$reference_genome.own_file" genome.fa && |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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33 #set index_path = 'genome' |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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34 #else: |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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35 #set index_path = $reference_genome.index.fields.path |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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36 #end if |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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37 hicup_digester --re1 '$re1' --genome '$genome' |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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38 #if $advanced_options.re2: |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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39 --re2 '$advanced_options.re2' |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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40 #end if |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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41 #for $file in $input_files_digest: |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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42 $file |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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43 #end for |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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44 && mv *Digest_* digest_file.txt |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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45 && hicup |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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46 --zip |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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47 --threads \${GALAXY_SLOTS:-1} |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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48 --digest digest_file.txt |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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49 --index '$index_path' |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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50 --bowtie2 \$BOWTIE_PATH_BASH |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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51 $advanced_options.nofill --keep |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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52 |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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53 #if $advanced_options.longest: |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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54 --longest '$advanced_options.longest' |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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55 #end if |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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56 |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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57 #if $advanced_options.shortest: |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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58 --shortest '$advanced_options.shortest' |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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59 #end if |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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60 |
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61 $input1 $input2 |
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62 |
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63 && ls -al |
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64 ]]></command> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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65 <inputs> |
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66 <expand macro="input_files" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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67 <param name="input_files_digest" type="data" multiple="true" format="fasta" label="Input DNA sequence files that should be digested"/> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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68 <param argument="--genome" type="text" label="Genome name" |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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69 help="Name of the genome to be digested."/> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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70 <expand macro="re1" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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71 <expand macro="reference_genome_macro" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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72 <section name="advanced_options" title="Advanced options"> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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73 <expand macro="re2" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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74 <expand macro="filter_longest_shortest" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit c546c919808a853d3e1556cb28bb4a5f7e1f9932
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75 <expand macro="no_fill" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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76 </section> |
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77 </inputs> |
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78 <outputs> |
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79 <!-- Regular output of hicup --> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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80 <data name="hicup_results" format="html" from_work_dir="*.html" label="HiCUP results"/> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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81 <data name="hicup_report" format="txt" from_work_dir="HiCUP_summary_report*.txt" label="HiCUP report" /> |
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82 <data name="dataset_hicup" format="qname_sorted.bam" from_work_dir="*.hicup.*bam" label="HiCUP data result"/> |
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83 |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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84 <collection name="intermediate_results" label="HiCUP intermediate results" type="list"> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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85 <!-- Output of the truncater step --> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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86 <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary*.txt" /> |
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87 <data name="dataset1_trunc" format="fastq.gz" label="Hicup Dataset1 Truncation" from_work_dir="dataset1*.trunc.fastq.gz" /> |
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88 <data name="dataset2_trunc" format="fastq.gz" label="Hicup Dataset2 Truncation" from_work_dir="dataset2*.trunc.fastq.gz" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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89 <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1*.truncation_barchart.svg" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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90 <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2*.truncation_barchart.svg" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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91 <!-- Output of the mapper step --> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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92 <data name="hicup_mapper_summary" format="txt" from_work_dir="hicup_mapper_summary*" label="hicup_mapper_summary.txt"/> |
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93 <data name="result_pair" format="qname_sorted.bam" from_work_dir="*pair.bam" label="pair.bam"/> |
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94 <data name="dataset1_mapper_barchart" format="svg" from_work_dir="dataset1*.mapper_barchart.svg" label="Mapper Dataset1 Barchart.svg" /> |
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95 <data name="dataset2_mapper_barchart" format="svg" from_work_dir="dataset2*.mapper_barchart.svg" label="Mapper Dataset2 Barchart.svg" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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96 <!-- Output of the filter step --> |
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97 <data name="dataset_filt" format="qname_sorted.bam" from_work_dir="*.filt.bam" label="filt.bam" /> |
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98 <data name="hicup_filter_summary" format="txt" from_work_dir="hicup_filter_summary*.txt" label="hicup_filter_summary.txt" /> |
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99 <data name="contiguous_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*contiguous.filter.bam" label="contiguous.filter.bam" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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100 <data name="re_ligation_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*re_ligation.filter.bam" label="re_ligation.filter.bam" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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101 <data name="same_dangling_ends_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_dangling_ends.filter.bam" label="same_dangling_ends.filter.bam" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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102 <data name="invalid_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*invalid.filter.bam" label="invalid.filter.bam" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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103 <data name="same_circularised_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_circularised.filter.bam" label="same_circularised.filter.bam" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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104 <data name="same_internal_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*same_internal.filter.bam" label="same_internal.filter.bam" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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105 <data name="wrong_size_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*wrong_size.filter.bam" label="wrong_size.filter.bam"/> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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106 <data name="filter_piechart" format="svg" from_work_dir="*filter_piechart.svg" label="Filter piechart" /> |
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107 <data name="ditag_size_distribution" format="svg" from_work_dir="*.ditag_size_distribution.svg" label="Ditag size distribution" /> |
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108 <!-- Output of the deduplicator step --> |
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109 <data name="cis_trans_piechart" format="svg" from_work_dir="*deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/> |
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110 <data name="uniques_barchart" format="svg" from_work_dir="*deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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111 <data name="hicup_deduplicator_summary" format="txt" from_work_dir="hicup_deduplicator_summary*.txt" label="Hicup Deduplicator Summary" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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112 </collection> |
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113 </outputs> |
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114 <tests> |
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115 <test> |
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116 <!-- inputs --> |
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117 <param name="input_first_sequence" value="dataset1.fastq" ftype="fastq"/> |
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118 <param name="input_second_sequence" value="dataset2.fastq" ftype="fastq"/> |
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119 <param name="re1" value="A^AGCTT"/> |
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120 <param name="input_files_digest" value="chr21And22FromHg38.fasta"/> |
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121 <param name="genome" value="chr21And22FromHg38"/> |
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122 <conditional name="reference_genome"> |
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123 <param name="source" value="history" /> |
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124 <param name="own_file" value="chr21And22FromHg38.fasta"/> |
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125 </conditional> |
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126 |
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127 <!-- outputs --> |
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128 <output name="hicup_results" file="HiCUP_summary_report.html" ftype="html" lines_diff="10000"/> |
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129 <output name="dataset_hicup" file="dataset1_2.hicup.bam" lines_diff="10" ftype="qname_sorted.bam" /> |
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130 <output name="hicup_report" file="HiCUP_summary_report.txt" lines_diff="2"/> |
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131 |
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132 <output_collection name="intermediate_results"> |
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133 <!-- truncater step--> |
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134 <element name="hicup_truncater_summary" file="hicup_truncater_summary.txt" lines_diff="8"/> |
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135 <element name="dataset1_trunc" file="dataset1.trunc.fastq.gz" compare="sim_size"/> |
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136 <element name="dataset2_trunc" file="dataset2.trunc.fastq.gz" compare="sim_size"/> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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137 <element name="dataset1_truncater_barchart" file="dataset1.truncation_barchart.svg" ftype="svg" lines_diff="1000" /> |
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138 <element name="dataset2_truncater_barchart" file="dataset2.truncation_barchart.svg" ftype="svg" lines_diff="1000" /> |
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139 |
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140 <!-- mapper step --> |
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141 <element name="hicup_mapper_summary" file="hicup_mapper_summary.txt" lines_diff="4"/> |
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142 <element name="result_pair" file="dataset1_2.pair.bam" lines_diff="8" ftype="qname_sorted.bam"/> |
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143 <element name="dataset1_mapper_barchart" file="dataset1.mapper_barchart.svg" ftype="svg" lines_diff="1000"/> |
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144 <element name="dataset2_mapper_barchart" file="dataset2.mapper_barchart.svg" ftype="svg" lines_diff="1000"/> |
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145 |
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146 <!-- filter step--> |
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147 <element name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/> |
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148 <element name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
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149 <element name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
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150 <element name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
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151 <element name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
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152 <element name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
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153 <element name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
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154 <element name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
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155 <element name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" lines_diff="1000" /> |
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156 <element name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" lines_diff="1000" /> |
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157 |
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158 <!-- deduplicator step--> |
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159 <element name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" lines_diff="1000"/> |
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160 <element name="uniques_barchart" file="dataset1_2.filt.bam.deduplicator_uniques_barchart.svg" ftype="svg" lines_diff="1000"/> |
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161 <element name="hicup_deduplicator_summary" file="hicup_deduplicator_summary.txt" lines_diff="2"/> |
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162 </output_collection> |
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163 </test> |
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164 </tests> |
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165 <help><![CDATA[ |
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166 |
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167 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ |
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168 |
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169 To get more information about the pipeline visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#HiCUP |
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170 ]]></help> |
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171 <expand macro="citation_hicup" /> |
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172 </tool> |