Mercurial > repos > bgruening > hicup_filter
diff 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 |
line wrap: on
line diff
--- a/hicup_filter.xml Fri May 25 17:49:27 2018 -0400 +++ b/hicup_filter.xml Sat Oct 22 08:39:51 2022 +0000 @@ -1,4 +1,4 @@ -<tool id="hicup_filter" name="Hicup Filter" version="@VERSION@.0" profile="18.01"> +<tool id="hicup_filter" name="Hicup Filter" version="@VERSION@+galaxy0" profile="18.01"> <description>classifies read pairs, identifying valid Hi-C di-tags</description> <macros> <import>hicup_macros.xml</import> @@ -27,14 +27,14 @@ ]]></command> <inputs> <param name="inputFiles" type="data" multiple="true" format="sam,qname_sorted.bam" label="Input files in BAM or SAM fomat"/> - <param argument="--digest" type="data" format="txt" label="Genome digest file" help="Specify the genome digest file (created by hicup_digester)"/> + <param argument="--digest" type="data" format="tabular" label="Genome digest file" help="Specify the genome digest file (created by hicup_digester)"/> <section name="advanced_options" title="Advanced options"> <expand macro="filter_longest_shortest" /> </section> </inputs> <outputs> <data name="dataset_filt" format="qname_sorted.bam" from_work_dir="*.filt.bam" label="filt.bam" /> - <data name="hicup_filter_summary" format="txt" from_work_dir="hicup_filter_summary*.txt" label="hicup_filter_summary.txt" /> + <data name="hicup_filter_summary" format="tabular" from_work_dir="hicup_filter_summary*.txt" label="hicup_filter_summary.txt" /> <data name="contiguous_filter" format="qname_sorted.bam" from_work_dir="hicup_filter_ditag_rejects*/*contiguous.filter.bam" label="contiguous.filter.bam" /> <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" /> <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" /> @@ -48,24 +48,28 @@ <tests> <test> <param name="inputFiles" value="dataset1_2.pair.bam" ftype="qname_sorted.bam" /> - <param name="digest" value="digester_file.txt" ftype="txt" /> - <output name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/> - <output name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="8" ftype="qname_sorted.bam" /> - <output name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> - <output name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> - <output name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> - <output name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> - <output name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> - <output name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> - <output name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" lines_diff="1000" /> - <output name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" lines_diff="1000" /> + <param name="digest" value="digester_file.txt" ftype="tabular" /> + <output name="hicup_filter_summary"> + <assert_contents> + <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"/> + </assert_contents> + </output> + <output name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="11" ftype="qname_sorted.bam" /> + <output name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="11" ftype="qname_sorted.bam" /> + <output name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="11" ftype="qname_sorted.bam" /> + <output name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="11" ftype="qname_sorted.bam" /> + <output name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="11" ftype="qname_sorted.bam" /> + <output name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="11" ftype="qname_sorted.bam" /> + <output name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="11" ftype="qname_sorted.bam" /> + <output name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" compare="sim_size"/> + <output name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" compare="sim_size"/> </test> </tests> <help><![CDATA[ - For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ + For help please consult the documentation of HiCUP: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html - To get more information about the filter visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Filter + To get more information about the filter visit: https://www.bioinformatics.babraham.ac.uk/projects/hicup/read_the_docs/html/index.html#hicup-filter ]]></help> <expand macro="citation_hicup" /> </tool>