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annotate hicup_mapper.xml @ 1:7f6fa513960e draft

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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b4d9ad47b45abb117a059214e1f7b29d084b4ca3
author bgruening
date Sat, 19 Aug 2017 07:39:47 -0400
parents 9ba09ebeb5aa
children 320a2d826a00
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9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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1 <tool id="hicup_mapper" name="Hicup Mapper" version="0.1.0">
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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2 <description>aligns paired reads independently to a reference genome and retains reads where both partners align.</description>
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3 <macros>
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4 <import>hicup_macros.xml</import>
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5 </macros>
9ba09ebeb5aa 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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7 <expand macro="stdio" />
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8
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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9 <command><![CDATA[
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10 BOWTIE_PATH_BASH="\$(which bowtie2)" &&
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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11 #set index_path = ''
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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12 #if str($reference_genome.source) == "history":
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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13 bowtie2-build "$reference_genome.own_file" genome &&
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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14 ln -s "$reference_genome.own_file" genome.fa &&
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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15 #set index_path = 'genome'
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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16 #else:
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17 #set index_path = $reference_genome.index.fields.path
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18 #end if
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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19 hicup_mapper
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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20 --index '$index_path'
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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21 --bowtie2 \$BOWTIE_PATH_BASH
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22
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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23 $input_first_sequence $input_second_sequence
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24
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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25 ## output handling
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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26 && mv hicup_mapper_summary* hicup_mapper_summary.txt
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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27 && mv *.pair.sam result.pair.sam
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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28 && trunc_result_1=\$(echo '$input_first_sequence' | rev | cut -d'/' -f1 | rev)
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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29 && trunc_result_2=\$(echo '$input_second_sequence' | rev | cut -d'/' -f1 | rev)
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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30 && mv \$trunc_result_1*.mapper_barchart.svg dataset1.mapper_barchart.svg
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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31 && mv \$trunc_result_2*.mapper_barchart.svg dataset2.mapper_barchart.svg
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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32 && echo \$trunc_result_1.mapper_barchart.svg
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33 && echo \$trunc_result_2.mapper_barchart.svg
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34 ]]></command>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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35 <inputs>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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36 <expand macro="input_files" />
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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37 <expand macro="reference_genome_macro" />
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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38 </inputs>
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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39 <outputs>
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40 <expand macro="mapper_output" />
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="input_first_sequence" value="dataset1.trunc.fastq" ftype="fastq"/>
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45 <param name="input_second_sequence" value="dataset2.trunc.fastq" ftype="fastq"/>
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46
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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47 <conditional name="reference_genome">
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48 <param name="source" value="history" />
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49 <param name="own_file" value="chr1.fa"/>
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50 </conditional>
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51 <output name="hicup_mapper_summary" file="hicup_mapper_summary.txt" lines_diff="4"/>
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52 <output name="result_pair" file="result.pair.sam" lines_diff="8"/>
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53 <output name="dataset1_mapper_barchart" file="dataset1.mapper_barchart.svg" ftype="svg" lines_diff="1000"/>
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54 <output name="dataset2_mapper_barchart" file="dataset2.mapper_barchart.svg" ftype="svg" lines_diff="1000"/>
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55
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56 </test>
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57 </tests>
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58 <help><![CDATA[
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59
9ba09ebeb5aa planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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60 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
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61
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62 To get more information about the mapper visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Mapper
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63 ]]></help>
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64 <expand macro="citation_hicup" />
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65 </tool>