Mercurial > repos > bgruening > hicup_filter

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 398a2e3e845ada656b3a7e0a6542e1668a8bcf17
author bgruening
date Thu, 23 Feb 2023 18:06:05 +0000
parents daf29b40670f
children
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1 <tool id="hicup_filter" name="Hicup Filter" version="@VERSION@+galaxy0" profile="18.01">
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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 <command detect_errors="exit_code"><![CDATA[
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8 #for $i, $file in enumerate($inputFiles):
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9 #if $file.ext != 'sam':
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10 ln -s '$file' ./${i}.bam &&
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11 #end if
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12 #end for
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13 hicup_filter --zip --digest '$digest'
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14 #if $advanced_options.longest:
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15 --longest '$advanced_options.longest'
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16 #end if
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17 #if $advanced_options.shortest:
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18 --shortest '$advanced_options.shortest'
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19 #end if
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20 #for $i, $file in enumerate($inputFiles):
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21 #if $file.ext != 'sam':
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22 ./${i}.bam
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23 #else:
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24 '$file'
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25 #end if
0
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26 #end for
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27 ]]></command>
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28 <inputs>
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29 <param name="inputFiles" type="data" multiple="true" format="sam,qname_sorted.bam" label="Input files in BAM or SAM fomat"/>
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30 <param argument="--digest" type="data" format="tabular" label="Genome digest file" help="Specify the genome digest file (created by hicup_digester)"/>
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31 <section name="advanced_options" title="Advanced options">
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32 <expand macro="filter_longest_shortest" />
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33 </section>
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34 </inputs>
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35 <outputs>
4
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36 <data name="dataset_filt" format="qname_sorted.bam" from_work_dir="*.filt.bam" label="filt.bam" />
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37 <data name="hicup_filter_summary" format="tabular" from_work_dir="hicup_filter_summary*.txt" label="hicup_filter_summary.txt" />
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38 <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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39 <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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40 <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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41 <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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42 <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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43 <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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44 <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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45 <data name="filter_piechart" format="svg" from_work_dir="*filter_piechart.svg" label="Filter piechart" />
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46 <data name="ditag_size_distribution" format="svg" from_work_dir="*.ditag_size_distribution.svg" label="Ditag size distribution" />
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47 </outputs>
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48 <tests>
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49 <test>
4
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50 <param name="inputFiles" value="dataset1_2.pair.bam" ftype="qname_sorted.bam" />
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51 <param name="digest" value="digest_file.txt" ftype="tabular" />
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52 <output name="hicup_filter_summary">
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53 <assert_contents>
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54 <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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55 </assert_contents>
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56 </output>
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57 <output name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="11" ftype="qname_sorted.bam" />
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58 <output name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="11" ftype="qname_sorted.bam" />
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59 <output name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="11" ftype="qname_sorted.bam" />
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60 <output name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="11" ftype="qname_sorted.bam" />
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61 <output name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="11" ftype="qname_sorted.bam" />
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62 <output name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="11" ftype="qname_sorted.bam" />
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63 <output name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="11" ftype="qname_sorted.bam" />
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64 <output name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" compare="sim_size"/>
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65 <output name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" compare="sim_size"/>
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66 </test>
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67 </tests>
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68 <help><![CDATA[
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69
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70 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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71
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72 To get more information about the filter visit: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-filter
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73 ]]></help>
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74 <expand macro="citation_hicup" />
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75 </tool>