Mercurial > repos > bgruening > hicup_filter
comparison hicup_filter.xml @ 4:a7bbbf32da62 draft
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
author | bgruening |
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date | Fri, 25 May 2018 17:49:27 -0400 |
parents | b16228ec1540 |
children | daf29b40670f |
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3:b16228ec1540 | 4:a7bbbf32da62 |
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1 <tool id="hicup_filter" name="Hicup Filter" version="@VERSION@.0"> | 1 <tool id="hicup_filter" name="Hicup Filter" version="@VERSION@.0" 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"/> |
7 <expand macro="stdio" /> | 7 <command detect_errors="exit_code"><![CDATA[ |
8 <command><![CDATA[ | 8 #for $i, $file in enumerate($inputFiles): |
9 hicup_filter --digest '$digest' | 9 #if $file.ext != 'sam': |
10 ln -s '$file' ./${i}.bam && | |
11 #end if | |
12 #end for | |
13 hicup_filter --zip --digest '$digest' | |
10 #if $advanced_options.longest: | 14 #if $advanced_options.longest: |
11 --longest '$advanced_options.longest' | 15 --longest '$advanced_options.longest' |
12 #end if | 16 #end if |
13 #if $advanced_options.shortest: | 17 #if $advanced_options.shortest: |
14 --shortest '$advanced_options.shortest' | 18 --shortest '$advanced_options.shortest' |
15 #end if | 19 #end if |
16 #for $file in $inputFiles: | 20 #for $i, $file in enumerate($inputFiles): |
17 $file | 21 #if $file.ext != 'sam': |
22 ./${i}.bam | |
23 #else: | |
24 '$file' | |
25 #end if | |
18 #end for | 26 #end for |
19 && mv hicup_filter_ditag_rejects* hicup_filter_ditag_rejects | |
20 && mv *filt.sam dataset.filt.sam | |
21 && mv hicup_filter_summary* hicup_filter_summary.txt | |
22 && mv hicup_filter_ditag_rejects/*contiguous.filter.sam hicup_filter_ditag_rejects/dataset.contiguous.filter.sam | |
23 && mv hicup_filter_ditag_rejects/*re_ligation.filter.sam hicup_filter_ditag_rejects/dataset.re_ligation.filter.sam | |
24 && mv hicup_filter_ditag_rejects/*same_dangling_ends.filter.sam hicup_filter_ditag_rejects/dataset.same_dangling_ends.filter.sam | |
25 && mv hicup_filter_ditag_rejects/*invalid.filter.sam hicup_filter_ditag_rejects/dataset.invalid.filter.sam | |
26 && mv hicup_filter_ditag_rejects/*same_circularised.filter.sam hicup_filter_ditag_rejects/dataset.same_circularised.filter.sam | |
27 && mv hicup_filter_ditag_rejects/*same_internal.filter.sam hicup_filter_ditag_rejects/dataset.same_internal.filter.sam | |
28 #if $advanced_options.longest or $advanced_options.shortest: | |
29 && mv hicup_filter_ditag_rejects/*wrong_size.filter.sam hicup_filter_ditag_rejects/dataset.wrong_size.filter.sam | |
30 #end if | |
31 | |
32 && mv *filter_piechart.svg filter_piechart.svg | |
33 ]]></command> | 27 ]]></command> |
34 <inputs> | 28 <inputs> |
35 <param name="inputFiles" type="data" multiple="true" format="bam,sam" label="Input"/> | 29 <param name="inputFiles" type="data" multiple="true" format="sam,qname_sorted.bam" label="Input files in BAM or SAM fomat"/> |
36 <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="txt" label="Genome digest file" help="Specify the genome digest file (created by hicup_digester)"/> |
37 <section name="advanced_options" title="Advanced options"> | 31 <section name="advanced_options" title="Advanced options"> |
38 <expand macro="filter_longest_shortest" /> | 32 <expand macro="filter_longest_shortest" /> |
39 </section> | 33 </section> |
40 </inputs> | 34 </inputs> |
41 <outputs> | 35 <outputs> |
42 <expand macro="filter_output" /> | 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" /> | |
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" /> | |
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" /> | |
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" /> | |
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" /> | |
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"/> | |
45 <data name="filter_piechart" format="svg" from_work_dir="*filter_piechart.svg" label="Filter piechart" /> | |
46 <data name="ditag_size_distribution" format="svg" from_work_dir="*.ditag_size_distribution.svg" label="Ditag size distribution" /> | |
43 </outputs> | 47 </outputs> |
44 <tests> | 48 <tests> |
45 <test> | 49 <test> |
50 <param name="inputFiles" value="dataset1_2.pair.bam" ftype="qname_sorted.bam" /> | |
46 <param name="digest" value="digester_file.txt" ftype="txt" /> | 51 <param name="digest" value="digester_file.txt" ftype="txt" /> |
47 <param name="inputFiles" value="result.pair.sam" ftype="sam" /> | |
48 <output name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/> | 52 <output name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/> |
49 <output name="dataset_filt" file="dataset.filt.sam" lines_diff="8" /> | 53 <output name="dataset_filt" file="dataset1_2.filt.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
50 <output name="contiguous_filter" file="dataset.contiguous.filter.sam" lines_diff="8" /> | 54 <output name="contiguous_filter" file="dataset1_2_contiguous.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
51 <output name="re_ligation_filter" file="dataset.re_ligation.filter.sam" lines_diff="8" /> | 55 <output name="re_ligation_filter" file="dataset1_2_re_ligation.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
52 <output name="same_dangling_ends_filter" file="dataset.same_dangling_ends.filter.sam" lines_diff="8" /> | 56 <output name="same_dangling_ends_filter" file="dataset1_2_same_dangling_ends.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
53 <output name="invalid_filter" file="dataset.invalid.filter.sam" lines_diff="8" /> | 57 <output name="invalid_filter" file="dataset1_2_invalid.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
54 <output name="same_circularised_filter" file="dataset.same_circularised.filter.sam" lines_diff="8" /> | 58 <output name="same_circularised_filter" file="dataset1_2_same_circularised.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
55 <output name="same_internal_filter" file="dataset.same_internal.filter.sam" lines_diff="8" /> | 59 <output name="same_internal_filter" file="dataset1_2_same_internal.filter.bam" lines_diff="8" ftype="qname_sorted.bam" /> |
56 <output name="filter_piechart" file="filter_piechart.svg" ftype="svg" lines_diff="1000" /> | 60 <output name="filter_piechart" file="dataset1_2.pair.bam.filter_piechart.svg" ftype="svg" lines_diff="1000" /> |
61 <output name="ditag_size_distribution" file="dataset1_2.ditag_size_distribution.svg" ftype="svg" lines_diff="1000" /> | |
57 </test> | 62 </test> |
58 </tests> | 63 </tests> |
59 <help><![CDATA[ | 64 <help><![CDATA[ |
60 | 65 |
61 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ | 66 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ |