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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
author bgruening
date Sat, 22 Oct 2022 08:38:32 +0000
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a5934ac7c399 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
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1 <tool id="hicup_deduplicator" name="Hicup Deduplicator" version="@VERSION@+galaxy0" profile="18.01">
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2 <description>removes duplicated di-tags (retaining one copy of each) from the data set.</description>
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3 <macros>
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4 <import>hicup_macros.xml</import>
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5 </macros>
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6 <expand macro="requirements_hicup" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 #if $input_file.ext != 'sam':
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9 ln -s '$input_file' input.bam &&
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10 #end if
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11 hicup_deduplicator --zip --quiet
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12 #if $input_file.ext != 'sam':
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13 input.bam
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14 #else
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15 '$input_file'
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16 #end if
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17 ]]></command>
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18 <inputs>
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19 <param name="input_file" type="data" format="qname_sorted.bam,sam" label="Input file(s)" help="Input files in BAM or SAM format."/>
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20 </inputs>
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21 <outputs>
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22 <data name="dedup_result" format="qname_sorted.bam" label="Deduplicator Result" from_work_dir="*dedup*.bam" />
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23 <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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24 <data name="uniques_barchart" format="svg" from_work_dir="*deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" />
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25 <data name="hicup_deduplicator_summary" format="tabular" from_work_dir="hicup_deduplicator_summary*.txt" label="Hicup Deduplicator Summary" />
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26 </outputs>
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27 <tests>
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28 <test>
4
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29 <param name="input_file" value="dataset1_2.filt.bam" ftype="qname_sorted.bam"/>
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30 <output name="dedup_result" file="dataset1_2.hicup.bam" compare="sim_size" ftype="qname_sorted.bam"/>
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31 <output name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" compare="sim_size"/>
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32 <output name="uniques_barchart" file="dataset1_2.filt.bam.deduplicator_uniques_barchart.svg" ftype="svg" compare="sim_size"/>
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33 <output name="hicup_deduplicator_summary">
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34 <assert_contents>
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35 <has_text_matching expression="\s+544\s+544\s+44\s+440\s+60"/>
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36 </assert_contents>
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37 </output>
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38 </test>
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39 <test>
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40 <param name="input_file" value="dataset1_2.filt.sam" ftype="sam"/>
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41 <output name="dedup_result" file="dataset1_2.hicup.bam" compare="sim_size" ftype="qname_sorted.bam"/>
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42 <output name="cis_trans_piechart" file="dataset1_2.filt.bam.deduplicator_cis_trans_piechart.svg" ftype="svg" compare="sim_size" delta="50000" />
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43 <output name="uniques_barchart" file="dataset1_2.filt.bam.deduplicator_uniques_barchart.svg" ftype="svg" compare="sim_size"/>
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44 <output name="hicup_deduplicator_summary">
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45 <assert_contents>
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46 <has_text_matching expression="\s+544\s+544\s+44\s+440\s+60"/>
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47 </assert_contents>
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48 </output>
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49 </test>
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50 </tests>
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51 <help><![CDATA[
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52
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53 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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54
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55 To get more information about the deduplicator visit: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-deduplicator
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56 ]]></help>
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57 <expand macro="citation_hicup" />
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58 </tool>