Mercurial > repos > bgruening > hicup_filter
comparison hicup_filter.xml @ 0:566da23a5a08 draft
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
author | bgruening |
---|---|
date | Thu, 09 Mar 2017 09:31:25 -0500 |
parents | |
children | cfa9c047cda4 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:566da23a5a08 |
---|---|
1 <tool id="hicup_filter" name="Hicup Filter" version="0.1.0"> | |
2 <description>classifies read pairs, identifying valid Hi-C di-tags.</description> | |
3 | |
4 <macros> | |
5 <import>hicup_macros.xml</import> | |
6 </macros> | |
7 <expand macro="requirements_hicup" /> | |
8 <expand macro="stdio" /> | |
9 | |
10 <command><![CDATA[ | |
11 hicup_filter --digest '$digest' | |
12 #if $advanced_options.longest: | |
13 --longest '$advanced_options.longest' | |
14 #end if | |
15 #if $advanced_options.shortest: | |
16 --shortest '$advanced_options.shortest' | |
17 #end if | |
18 #for $file in $inputFiles: | |
19 $file | |
20 #end for | |
21 && mv hicup_filter_ditag_rejects* hicup_filter_ditag_rejects | |
22 && mv *filt.sam dataset.filt.sam | |
23 && mv hicup_filter_summary* hicup_filter_summary.txt | |
24 && mv hicup_filter_ditag_rejects/*contiguous.filter.sam hicup_filter_ditag_rejects/dataset.contiguous.filter.sam | |
25 && mv hicup_filter_ditag_rejects/*re_ligation.filter.sam hicup_filter_ditag_rejects/dataset.re_ligation.filter.sam | |
26 && mv hicup_filter_ditag_rejects/*same_dangling_ends.filter.sam hicup_filter_ditag_rejects/dataset.same_dangling_ends.filter.sam | |
27 && mv hicup_filter_ditag_rejects/*invalid.filter.sam hicup_filter_ditag_rejects/dataset.invalid.filter.sam | |
28 && mv hicup_filter_ditag_rejects/*same_circularised.filter.sam hicup_filter_ditag_rejects/dataset.same_circularised.filter.sam | |
29 && mv hicup_filter_ditag_rejects/*same_internal.filter.sam hicup_filter_ditag_rejects/dataset.same_internal.filter.sam | |
30 #if $advanced_options.longest or $advanced_options.shortest: | |
31 && mv hicup_filter_ditag_rejects/*wrong_size.filter.sam hicup_filter_ditag_rejects/dataset.wrong_size.filter.sam | |
32 #end if | |
33 | |
34 && mv *filter_piechart.svg filter_piechart.svg | |
35 ]]></command> | |
36 <inputs> | |
37 <param name="inputFiles" type="data" multiple="true" format="bam,sam" label="Input"/> | |
38 <param argument="--digest" type="data" format="txt" label="Genome digest file" help="Specify the genome digest file (created by hicup_digester)"/> | |
39 <section name="advanced_options" title="Advanced options"> | |
40 <expand macro="filter_longest_shortest" /> | |
41 </section> | |
42 </inputs> | |
43 <outputs> | |
44 <expand macro="filter_output" /> | |
45 </outputs> | |
46 <tests> | |
47 <test> | |
48 <param name="digest" value="digester_file.txt" ftype="txt" /> | |
49 <param name="inputFiles" value="result.pair.sam" ftype="sam" /> | |
50 <output name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/> | |
51 <output name="dataset_filt" file="dataset.filt.sam" lines_diff="8" /> | |
52 <output name="contiguous_filter" file="dataset.contiguous.filter.sam" lines_diff="8" /> | |
53 <output name="re_ligation_filter" file="dataset.re_ligation.filter.sam" lines_diff="8" /> | |
54 <output name="same_dangling_ends_filter" file="dataset.same_dangling_ends.filter.sam" lines_diff="8" /> | |
55 <output name="invalid_filter" file="dataset.invalid.filter.sam" lines_diff="8" /> | |
56 <output name="same_circularised_filter" file="dataset.same_circularised.filter.sam" lines_diff="8" /> | |
57 <output name="same_internal_filter" file="dataset.same_internal.filter.sam" lines_diff="8" /> | |
58 <output name="filter_piechart" file="filter_piechart.svg" ftype="svg" lines_diff="1000" /> | |
59 </test> | |
60 </tests> | |
61 <help><![CDATA[ | |
62 | |
63 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ | |
64 | |
65 To get more information about the filter visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#Filter | |
66 ]]></help> | |
67 <expand macro="citation_hicup" /> | |
68 </tool> |