Mercurial > repos > bgruening > hicup_hicup
annotate hicup_hicup.xml @ 7:68fb19094f84 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 398a2e3e845ada656b3a7e0a6542e1668a8bcf17
author | bgruening |
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date | Thu, 23 Feb 2023 18:04:00 +0000 |
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6137fb382a02
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
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1 <tool id="hicup_hicup" name="Hicup Pipeline" version="@VERSION@+galaxy0"> |
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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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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/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
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9 ##Dealing with inputs |
6137fb382a02
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
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10 @PAIRED-END_INPUT@ |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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11 |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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12 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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13 #set index_path = '' |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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14 #if str($reference_genome.source) == "history": |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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15 bowtie2-build "$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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16 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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17 #set index_path = 'genome' |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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18 #else: |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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19 #set index_path = $reference_genome.index.fields.path |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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20 #end if |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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21 hicup_digester --re1 '$re1' --genome '$genome' |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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22 #if $advanced_options.re2: |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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23 --re2 '$advanced_options.re2' |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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24 #end if |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
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25 '$index_path'.fa |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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26 && mv *Digest_* digest_file.txt |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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27 && hicup |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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28 --zip |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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29 --threads \${GALAXY_SLOTS:-1} |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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30 --digest digest_file.txt |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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31 --index '$index_path' |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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32 --bowtie2 \$BOWTIE_PATH_BASH |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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33 $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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34 |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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35 #if $advanced_options.longest: |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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36 --longest '$advanced_options.longest' |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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37 #end if |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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38 |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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39 #if $advanced_options.shortest: |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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40 --shortest '$advanced_options.shortest' |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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41 #end if |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
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42 '$read1' |
6137fb382a02
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
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43 '$read2' |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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44 ]]></command> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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45 <inputs> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
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46 <expand macro="input_paired"/> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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47 <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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48 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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49 <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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50 <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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51 <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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52 <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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53 <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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54 <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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55 </section> |
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56 </inputs> |
7e9e8da0522d
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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57 <outputs> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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58 <!-- Regular output of hicup --> |
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59 <data name="hicup_results" format="html" from_work_dir="*.html" label="HiCUP report (html)"/> |
6137fb382a02
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
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60 <data name="hicup_report" format="tabular" from_work_dir="HiCUP_summary_report*.txt" label="HiCUP report (txt)" /> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
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61 <data name="dataset_hicup" format="qname_sorted.bam" from_work_dir="*.hicup.*bam" label="HiCUP result (BAM)"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
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62 <data name="digester_file" format="tabular" from_work_dir="digest_file.txt" label="Digester file"/> |
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63 |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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64 <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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65 <!-- Output of the truncater step --> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
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66 <data name="hicup_truncater_summary" format="tabular" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary*.txt" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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67 <data name="dataset1_trunc" format="fastq.gz" label="Hicup Dataset1 Truncation" from_work_dir="dataset1*.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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68 <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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69 <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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70 <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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71 <!-- Output of the mapper step --> |
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72 <data name="hicup_mapper_summary" format="tabular" from_work_dir="hicup_mapper_summary*" label="hicup_mapper_summary.txt"/> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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73 <data name="result_pair" format="qname_sorted.bam" from_work_dir="*pair.bam" label="pair.bam"/> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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74 <data name="dataset1_mapper_barchart" format="svg" from_work_dir="dataset1*.mapper_barchart.svg" label="Mapper Dataset1 Barchart.svg" /> |
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75 <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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76 <!-- Output of the filter step --> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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77 <data name="dataset_filt" format="qname_sorted.bam" from_work_dir="*.filt.bam" label="filt.bam" /> |
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78 <data name="hicup_filter_summary" format="tabular" from_work_dir="hicup_filter_summary*.txt" label="hicup_filter_summary.txt" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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79 <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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80 <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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81 <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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82 <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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83 <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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84 <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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85 <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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86 <data name="filter_piechart" format="svg" from_work_dir="*filter_piechart.svg" label="Filter piechart" /> |
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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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87 <data name="ditag_size_distribution" format="svg" from_work_dir="*.ditag_size_distribution.svg" label="Ditag size distribution" /> |
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88 <data name="ditag_size_distribution_txt" format="tabular" from_work_dir="*.ditag_size_distribution_report.txt" label="Report of ditag size distribution" /> |
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89 <!-- Output of the deduplicator step --> |
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90 <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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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
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91 <data name="uniques_barchart" format="svg" from_work_dir="*deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" /> |
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92 <data name="hicup_deduplicator_summary" format="tabular" 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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93 </collection> |
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94 </outputs> |
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95 <tests> |
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96 <test> |
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97 <!-- inputs --> |
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98 <conditional name="library"> |
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99 <param name="type" value="paired"/> |
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100 <param name="input_1" value="dataset1.fastq" ftype="fastq"/> |
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101 <param name="input_2" value="dataset2.fastq" ftype="fastq"/> |
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102 </conditional> |
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103 <param name="re1" value="A^AGCTT"/> |
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104 <param name="genome" value="chr21And22FromHg38"/> |
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105 <conditional name="reference_genome"> |
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106 <param name="source" value="history" /> |
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107 <param name="own_file" value="chr21And22FromHg38.fasta"/> |
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108 </conditional> |
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109 |
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110 <!-- outputs --> |
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111 <output name="hicup_results"> |
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112 <assert_contents> |
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113 <has_size value="4681214" delta="400000"/> |
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114 <has_text text="HiCUP Summary Report"/> |
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115 </assert_contents> |
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116 </output> |
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117 <output name="dataset_hicup" file="dataset1_2.hicup.bam" compare="sim_size" ftype="qname_sorted.bam" /> |
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118 <output name="hicup_report" file="HiCUP_summary_report_aQdQORylpl_22-59-39_22-02-2023.txt" lines_diff="0"/> |
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119 <output name="digester_file" file="digest_file.txt" lines_diff="0"/> |
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120 |
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121 <output_collection name="intermediate_results"> |
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122 <!-- truncater step--> |
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123 <element name="hicup_truncater_summary"> |
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124 <assert_contents> |
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125 <has_text_matching expression="\s+99742\s+7230\s+7.25\s+92512\s+92.75\s+22.45"/> |
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126 <has_text_matching expression="\s+99742\s+7114\s+7.13\s+92628\s+92.87\s+22.63"/> |
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127 </assert_contents> |
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128 </element> |
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129 <element name="dataset1_trunc" file="dataset1.trunc.fastq.gz" decompress="true"/> |
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130 <element name="dataset2_trunc" file="dataset2.trunc.fastq.gz" decompress="true"/> |
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131 <element name="dataset1_truncater_barchart" file="dataset1.fastq.truncation_barchart.svg" ftype="svg" compare="sim_size" /> |
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132 <element name="dataset2_truncater_barchart" file="dataset2.fastq.truncation_barchart.svg" ftype="svg" compare="sim_size" /> |
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133 |
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134 <!-- mapper step --> |
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135 <element name="hicup_mapper_summary"> |
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136 <assert_contents> |
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137 <has_text_matching expression="\s+99742\s+2658\s+2.7\s+3885\s+3.9\s+12437\s+12.5\s+80762\s+81.0\s+1143\s+1.1"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
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138 <has_text_matching expression="\s+99742\s+2476\s+2.5\s+3725\s+3.7\s+12679\s+12.7\s+80862\s+81.1\s+1143\s+1.1"/> |
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139 </assert_contents> |
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140 </element> |
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141 <element name="result_pair" file="dataset1_2.pair.bam" lines_diff="2" ftype="qname_sorted.bam"/> |
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142 <element name="dataset1_mapper_barchart" file="dataset1.trunc.fastq.gz.mapper_barchart.svg" ftype="svg" compare="sim_size" /> |
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143 <element name="dataset2_mapper_barchart" file="dataset2.trunc.fastq.gz.mapper_barchart.svg" ftype="svg" compare="sim_size" /> |
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144 |
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145 <!-- filter step--> |
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146 <element name="hicup_filter_summary"> |
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147 <assert_contents> |
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148 <has_text_matching expression="\s+1143\s+544\s+44\s+440\s+60\s+599\s+21\s+73\s+466\s+39\s+0\s+0"/> |
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149 </assert_contents> |
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150 </element> |
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151 <element name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="4" ftype="qname_sorted.bam" /> |
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152 <element name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> |
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153 <element name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> |
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154 <element name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> |
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155 <element name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> |
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156 <element name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> |
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157 <element name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="4" ftype="qname_sorted.bam" /> |
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158 <element name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" compare="sim_size" /> |
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159 <element name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" compare="sim_size" /> |
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160 <element name="ditag_size_distribution_txt" file="dataset1_2.ditag_size_distribution_report.txt" ftype="tabular"/> |
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161 |
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162 <!-- deduplicator step--> |
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163 <element name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" compare="sim_size" /> |
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164 <element name="uniques_barchart" file="dataset1_2.filt.bam.deduplicator_uniques_barchart.svg" ftype="svg" compare="sim_size" /> |
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165 <element name="hicup_deduplicator_summary" > |
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166 <assert_contents> |
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167 <has_text_matching expression="\s+544\s+544\s+44\s+440\s+60"/> |
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168 </assert_contents> |
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169 </element> |
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170 </output_collection> |
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171 </test> |
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172 </tests> |
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173 <help><![CDATA[ |
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174 |
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175 For help please consult the documentation of HiCUP: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html |
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176 |
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177 To get more information about the pipeline visit: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-pipeline-control-script |
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178 ]]></help> |
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179 <expand macro="citation_hicup" /> |
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180 </tool> |