Mercurial > repos > bgruening > hicup_filter
comparison hicup_filter.xml @ 5:daf29b40670f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/hicup commit 5466e3345d762ed53686d80568929c2e15652eef
| author | bgruening |
|---|---|
| date | Sat, 22 Oct 2022 08:39:51 +0000 |
| parents | a7bbbf32da62 |
| children | 2d4a34c00c67 |
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| 4:a7bbbf32da62 | 5:daf29b40670f |
|---|---|
| 1 <tool id="hicup_filter" name="Hicup Filter" version="@VERSION@.0" profile="18.01"> | 1 <tool id="hicup_filter" name="Hicup Filter" version="@VERSION@+galaxy0" profile="18.01"> |
| 2 <description>classifies read pairs, identifying valid Hi-C di-tags</description> | 2 <description>classifies read pairs, identifying valid Hi-C di-tags</description> |
| 3 <macros> | 3 <macros> |
| 4 <import>hicup_macros.xml</import> | 4 <import>hicup_macros.xml</import> |
| 5 </macros> | 5 </macros> |
| 6 <expand macro="requirements_hicup"/> | 6 <expand macro="requirements_hicup"/> |
| 25 #end if | 25 #end if |
| 26 #end for | 26 #end for |
| 27 ]]></command> | 27 ]]></command> |
| 28 <inputs> | 28 <inputs> |
| 29 <param name="inputFiles" type="data" multiple="true" format="sam,qname_sorted.bam" label="Input files in BAM or SAM fomat"/> | 29 <param name="inputFiles" type="data" multiple="true" format="sam,qname_sorted.bam" label="Input files in BAM or SAM fomat"/> |
| 30 <param argument="--digest" type="data" format="txt" label="Genome digest file" help="Specify the genome digest file (created by hicup_digester)"/> | 30 <param argument="--digest" type="data" format="tabular" label="Genome digest file" help="Specify the genome digest file (created by hicup_digester)"/> |
| 31 <section name="advanced_options" title="Advanced options"> | 31 <section name="advanced_options" title="Advanced options"> |
| 32 <expand macro="filter_longest_shortest" /> | 32 <expand macro="filter_longest_shortest" /> |
| 33 </section> | 33 </section> |
| 34 </inputs> | 34 </inputs> |
| 35 <outputs> | 35 <outputs> |
| 36 <data name="dataset_filt" format="qname_sorted.bam" from_work_dir="*.filt.bam" label="filt.bam" /> | 36 <data name="dataset_filt" format="qname_sorted.bam" from_work_dir="*.filt.bam" label="filt.bam" /> |
| 37 <data name="hicup_filter_summary" format="txt" from_work_dir="hicup_filter_summary*.txt" label="hicup_filter_summary.txt" /> | 37 <data name="hicup_filter_summary" format="tabular" from_work_dir="hicup_filter_summary*.txt" label="hicup_filter_summary.txt" /> |
| 38 <data name="contiguous_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*contiguous.filter.bam" label="contiguous.filter.bam" /> | 38 <data name="contiguous_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*contiguous.filter.bam" label="contiguous.filter.bam" /> |
| 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" /> | 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" /> |
| 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" /> | 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" /> |
| 41 <data name="invalid_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*invalid.filter.bam" label="invalid.filter.bam" /> | 41 <data name="invalid_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*invalid.filter.bam" label="invalid.filter.bam" /> |
| 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" /> | 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" /> |
| 46 <data name="ditag_size_distribution" format="svg" from_work_dir="*.ditag_size_distribution.svg" label="Ditag size distribution" /> | 46 <data name="ditag_size_distribution" format="svg" from_work_dir="*.ditag_size_distribution.svg" label="Ditag size distribution" /> |
| 47 </outputs> | 47 </outputs> |
| 48 <tests> | 48 <tests> |
| 49 <test> | 49 <test> |
| 50 <param name="inputFiles" value="dataset1_2.pair.bam" ftype="qname_sorted.bam" /> | 50 <param name="inputFiles" value="dataset1_2.pair.bam" ftype="qname_sorted.bam" /> |
| 51 <param name="digest" value="digester_file.txt" ftype="txt" /> | 51 <param name="digest" value="digester_file.txt" ftype="tabular" /> |
| 52 <output name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/> | 52 <output name="hicup_filter_summary"> |
| 53 <output name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="8" ftype="qname_sorted.bam" /> | 53 <assert_contents> |
| 54 <output name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> | 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"/> |
| 55 <output name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> | 55 </assert_contents> |
| 56 <output name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> | 56 </output> |
| 57 <output name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> | 57 <output name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="11" ftype="qname_sorted.bam" /> |
| 58 <output name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> | 58 <output name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="11" ftype="qname_sorted.bam" /> |
| 59 <output name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> | 59 <output name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="11" ftype="qname_sorted.bam" /> |
| 60 <output name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" lines_diff="1000" /> | 60 <output name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="11" ftype="qname_sorted.bam" /> |
| 61 <output name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" lines_diff="1000" /> | 61 <output name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="11" ftype="qname_sorted.bam" /> |
| 62 <output name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="11" ftype="qname_sorted.bam" /> | |
| 63 <output name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="11" ftype="qname_sorted.bam" /> | |
| 64 <output name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" compare="sim_size"/> | |
| 65 <output name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" compare="sim_size"/> | |
| 62 </test> | 66 </test> |
| 63 </tests> | 67 </tests> |
| 64 <help><![CDATA[ | 68 <help><![CDATA[ |
| 65 | 69 |
| 66 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ | 70 For help please consult the documentation of HiCUP: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html |
| 67 | 71 |
| 68 To get more information about the filter visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Filter | 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 |
| 69 ]]></help> | 73 ]]></help> |
| 70 <expand macro="citation_hicup" /> | 74 <expand macro="citation_hicup" /> |
| 71 </tool> | 75 </tool> |