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annotate hicup_filter.xml @ 3:b16228ec1540 draft

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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit e6a9507eb198c6bf2c63ddae387c262bfc8dbd16
author bgruening
date Thu, 09 Nov 2017 11:16:04 -0500
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children a7bbbf32da62
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cfa9c047cda4 planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit c546c919808a853d3e1556cb28bb4a5f7e1f9932
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1 <tool id="hicup_filter" name="Hicup Filter" version="@VERSION@.0">
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2 <description>classifies read pairs, identifying valid Hi-C di-tags.</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 <expand macro="stdio" />
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8 <command><![CDATA[
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9 hicup_filter --digest '$digest'
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10 #if $advanced_options.longest:
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11 --longest '$advanced_options.longest'
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12 #end if
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13 #if $advanced_options.shortest:
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14 --shortest '$advanced_options.shortest'
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15 #end if
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16 #for $file in $inputFiles:
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17 $file
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18 #end for
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19 && mv hicup_filter_ditag_rejects* hicup_filter_ditag_rejects
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20 && mv *filt.sam dataset.filt.sam
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21 && mv hicup_filter_summary* hicup_filter_summary.txt
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22 && mv hicup_filter_ditag_rejects/*contiguous.filter.sam hicup_filter_ditag_rejects/dataset.contiguous.filter.sam
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23 && mv hicup_filter_ditag_rejects/*re_ligation.filter.sam hicup_filter_ditag_rejects/dataset.re_ligation.filter.sam
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24 && mv hicup_filter_ditag_rejects/*same_dangling_ends.filter.sam hicup_filter_ditag_rejects/dataset.same_dangling_ends.filter.sam
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25 && mv hicup_filter_ditag_rejects/*invalid.filter.sam hicup_filter_ditag_rejects/dataset.invalid.filter.sam
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26 && mv hicup_filter_ditag_rejects/*same_circularised.filter.sam hicup_filter_ditag_rejects/dataset.same_circularised.filter.sam
566da23a5a08 planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
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27 && mv hicup_filter_ditag_rejects/*same_internal.filter.sam hicup_filter_ditag_rejects/dataset.same_internal.filter.sam
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28 #if $advanced_options.longest or $advanced_options.shortest:
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29 && mv hicup_filter_ditag_rejects/*wrong_size.filter.sam hicup_filter_ditag_rejects/dataset.wrong_size.filter.sam
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30 #end if
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31
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32 && mv *filter_piechart.svg filter_piechart.svg
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33 ]]></command>
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34 <inputs>
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35 <param name="inputFiles" type="data" multiple="true" format="bam,sam" label="Input"/>
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36 <param argument="--digest" type="data" format="txt" label="Genome digest file" help="Specify the genome digest file (created by hicup_digester)"/>
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37 <section name="advanced_options" title="Advanced options">
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38 <expand macro="filter_longest_shortest" />
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39 </section>
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40 </inputs>
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41 <outputs>
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42 <expand macro="filter_output" />
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="digest" value="digester_file.txt" ftype="txt" />
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47 <param name="inputFiles" value="result.pair.sam" ftype="sam" />
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48 <output name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/>
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49 <output name="dataset_filt" file="dataset.filt.sam" lines_diff="8" />
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50 <output name="contiguous_filter" file="dataset.contiguous.filter.sam" lines_diff="8" />
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51 <output name="re_ligation_filter" file="dataset.re_ligation.filter.sam" lines_diff="8" />
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52 <output name="same_dangling_ends_filter" file="dataset.same_dangling_ends.filter.sam" lines_diff="8" />
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53 <output name="invalid_filter" file="dataset.invalid.filter.sam" lines_diff="8" />
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54 <output name="same_circularised_filter" file="dataset.same_circularised.filter.sam" lines_diff="8" />
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55 <output name="same_internal_filter" file="dataset.same_internal.filter.sam" lines_diff="8" />
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56 <output name="filter_piechart" file="filter_piechart.svg" ftype="svg" lines_diff="1000" />
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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61 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/
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62
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63 To get more information about the filter visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Filter
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64 ]]></help>
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65 <expand macro="citation_hicup" />
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66 </tool>