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
comparison
equal deleted inserted replaced
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>