Mercurial > repos > bgruening > hicup_hicup
comparison hicup_hicup.xml @ 0:7e9e8da0522d draft
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit b77cbc104261f8aa1524922f41c2a9a23052f5da
author | bgruening |
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date | Thu, 09 Mar 2017 09:31:57 -0500 |
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children | e96cb39c3f8e |
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-1:000000000000 | 0:7e9e8da0522d |
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1 <tool id="hicup_hicup" name="Hicup Pipeline" version="0.1.0"> | |
2 <description>controls the other programs in the HiCUP pipeline.</description> | |
3 <macros> | |
4 <import>hicup_macros.xml</import> | |
5 </macros> | |
6 <expand macro="requirements_hicup" /> | |
7 <expand macro="stdio" /> | |
8 | |
9 <command><![CDATA[ | |
10 | |
11 BOWTIE_PATH_BASH="\$(which bowtie2)" && | |
12 #set index_path = '' | |
13 #if str($reference_genome.source) == "history": | |
14 bowtie2-build "$reference_genome.own_file" genome && | |
15 ln -s "$reference_genome.own_file" genome.fa && | |
16 #set index_path = 'genome' | |
17 #else: | |
18 #set index_path = $reference_genome.index.fields.path | |
19 #end if | |
20 hicup_digester --re1 '$re1' --genome '$genome' | |
21 #if $advanced_options.re2: | |
22 --re2 '$advanced_options.re2' | |
23 #end if | |
24 #for $file in $input_files_digest: | |
25 $file | |
26 #end for | |
27 && mv *Digest_* digest_file.txt | |
28 && hicup | |
29 --digest digest_file.txt | |
30 --index '$index_path' | |
31 --bowtie2 \$BOWTIE_PATH_BASH | |
32 $advanced_options.nofill --keep | |
33 | |
34 #if $advanced_options.longest: | |
35 --longest '$advanced_options.longest' | |
36 #end if | |
37 | |
38 #if $advanced_options.shortest: | |
39 --shortest '$advanced_options.shortest' | |
40 #end if | |
41 | |
42 $input_first_sequence $input_second_sequence | |
43 | |
44 ## process truncater files | |
45 && ls -la | |
46 | |
47 && mv hicup_truncater_summary_* hicup_truncater_summary.txt | |
48 && trunc_result_1=\$(echo '$input_first_sequence' | rev | cut -d'/' -f1 | rev) | |
49 && mv \$trunc_result_1.truncation_barchart.svg dataset1.truncation_barchart.svg | |
50 && mv \$trunc_result_1.trunc.fastq dataset1.trunc.fastq | |
51 && trunc_result_2=\$(echo '$input_second_sequence' | rev | cut -d'/' -f1 | rev) | |
52 && mv \$trunc_result_2.truncation_barchart.svg dataset2.truncation_barchart.svg | |
53 && mv \$trunc_result_2.trunc.fastq dataset2.trunc.fastq | |
54 | |
55 && echo \$trunc_result_1 | |
56 && echo \$trunc_result_2 | |
57 | |
58 ## process mapper | |
59 && mv hicup_mapper_summary* hicup_mapper_summary.txt | |
60 && mv *.pair.sam result.pair.sam | |
61 | |
62 && mv \$trunc_result_1.trunc.fastq.mapper_barchart.svg dataset1.mapper_barchart.svg | |
63 && mv \$trunc_result_2.trunc.fastq.mapper_barchart.svg dataset2.mapper_barchart.svg | |
64 | |
65 | |
66 ## process filter | |
67 && mv hicup_filter_ditag_rejects* hicup_filter_ditag_rejects | |
68 && ls -la hicup_filter_ditag_rejects/ | |
69 && mv *filt.sam dataset.filt.sam | |
70 && mv hicup_filter_summary* hicup_filter_summary.txt | |
71 && mv hicup_filter_ditag_rejects/*contiguous.filter.sam hicup_filter_ditag_rejects/dataset.contiguous.filter.sam | |
72 && mv hicup_filter_ditag_rejects/*re_ligation.filter.sam hicup_filter_ditag_rejects/dataset.re_ligation.filter.sam | |
73 && mv hicup_filter_ditag_rejects/*same_dangling_ends.filter.sam hicup_filter_ditag_rejects/dataset.same_dangling_ends.filter.sam | |
74 && mv hicup_filter_ditag_rejects/*invalid.filter.sam hicup_filter_ditag_rejects/dataset.invalid.filter.sam | |
75 && mv hicup_filter_ditag_rejects/*same_circularised.filter.sam hicup_filter_ditag_rejects/dataset.same_circularised.filter.sam | |
76 && mv hicup_filter_ditag_rejects/*same_internal.filter.sam hicup_filter_ditag_rejects/dataset.same_internal.filter.sam | |
77 #if $advanced_options.longest or $advanced_options.shortest: | |
78 && mv hicup_filter_ditag_rejects/*wrong_size.filter.sam hicup_filter_ditag_rejects/dataset.wrong_size.filter.sam | |
79 #end if | |
80 && mv *pair.sam.filter_piechart.svg filter_piechart.svg | |
81 | |
82 ## deduplicator | |
83 && mv *filt.sam.deduplicator_cis_trans_piechart.svg deduplicator_cis_trans_piechart.svg | |
84 && mv *filt.sam.deduplicator_uniques_barchart.svg deduplicator_uniques_barchart.svg | |
85 && mv hicup_deduplicator_summary*.txt hicup_deduplicator_summary.txt | |
86 | |
87 ## process general output of hicup | |
88 && mv *.hicup.* dataset.hicup | |
89 && mv *.html results.html | |
90 && mv HiCUP_summary_report*.txt HiCUP_summary_report.txt | |
91 && ls -la | |
92 && ls -la hicup_filter_ditag_rejects/ | |
93 ]]></command> | |
94 <inputs> | |
95 <expand macro="input_files" /> | |
96 <expand macro="digester_input" /> | |
97 <expand macro="re1" /> | |
98 <expand macro="reference_genome_macro" /> | |
99 <section name="advanced_options" title="Advanced options"> | |
100 <expand macro="re2" /> | |
101 <expand macro="filter_longest_shortest" /> | |
102 <expand macro="no_fill" /> | |
103 </section> | |
104 </inputs> | |
105 <outputs> | |
106 <!-- Regular output of hicup --> | |
107 <data name="hicup_results" format="html" from_work_dir="results.html" label="HiCUP results"/> | |
108 <data name="hicup_report" format="txt" from_work_dir="HiCUP_summary_report.txt" label="HiCUP report" /> | |
109 <data name="dataset_hicup" format="bam,sam" from_work_dir="dataset.hicup" label="HiCUP data result"/> | |
110 | |
111 <collection name="intermediate_results" label="HiCUP intermediate results" type="list"> | |
112 <!-- Output of the truncater step --> | |
113 <expand macro="truncater_output" /> | |
114 <!-- Output of the mapper step --> | |
115 <expand macro="mapper_output" /> | |
116 <!-- Output of the filter step --> | |
117 <expand macro="filter_output" /> | |
118 <!-- Output of the deduplicator step --> | |
119 <expand macro="deduplicator_output" /> | |
120 </collection> | |
121 </outputs> | |
122 <tests> | |
123 <test> | |
124 <!-- inputs --> | |
125 <param name="input_first_sequence" value="dataset1.fastq" ftype="fastq"/> | |
126 <param name="input_second_sequence" value="dataset2.fastq" ftype="fastq"/> | |
127 <param name="re1" value="A^AGCTT"/> | |
128 <param name="input_files_digest" value="chr1.fa"/> | |
129 <param name="genome" value="human"/> | |
130 <conditional name="reference_genome"> | |
131 <param name="source" value="history" /> | |
132 <param name="own_file" value="chr1.fa"/> | |
133 </conditional> | |
134 | |
135 <!-- outputs --> | |
136 <output name="hicup_results" file="results.html" ftype="html" lines_diff="10000"/> | |
137 <output name="dataset_hicup" file="dataset.hicup.sam" lines_diff="5" /> | |
138 <output name="hicup_report" file="HiCUP_summary_report.txt" lines_diff="2"/> | |
139 | |
140 <output_collection name="intermediate_results"> | |
141 <!-- truncater step--> | |
142 <element name="hicup_truncater_summary" file="hicup_truncater_summary.txt" lines_diff="8"/> | |
143 <element name="dataset1_trunc" file="dataset1.trunc.fastq" lines_diff="8" /> | |
144 <element name="dataset2_trunc" file="dataset2.trunc.fastq" lines_diff="8"/> | |
145 <element name="dataset1_truncater_barchart" file="dataset1.truncation_barchart.svg" ftype="svg" lines_diff="1000" /> | |
146 <element name="dataset2_truncater_barchart" file="dataset2.truncation_barchart.svg" ftype="svg" lines_diff="1000" /> | |
147 | |
148 <!-- mapper step --> | |
149 <element name="hicup_mapper_summary" file="hicup_mapper_summary.txt" lines_diff="4"/> | |
150 <element name="result_pair" file="result.pair.sam" lines_diff="8"/> | |
151 <element name="dataset1_mapper_barchart" file="dataset1.mapper_barchart.svg" ftype="svg" lines_diff="1000"/> | |
152 <element name="dataset2_mapper_barchart" file="dataset2.mapper_barchart.svg" ftype="svg" lines_diff="1000"/> | |
153 | |
154 <!-- filter step--> | |
155 <element name="hicup_filter_summary" file="hicup_filter_summary.txt" lines_diff="12"/> | |
156 <element name="dataset_filt" file="dataset.filt.sam" lines_diff="8" /> | |
157 <element name="contiguous_filter" file="dataset.contiguous.filter.sam" lines_diff="8" /> | |
158 <element name="re_ligation_filter" file="dataset.re_ligation.filter.sam" lines_diff="8" /> | |
159 <element name="same_dangling_ends_filter" file="dataset.same_dangling_ends.filter.sam" lines_diff="8" /> | |
160 <element name="invalid_filter" file="dataset.invalid.filter.sam" lines_diff="8" /> | |
161 <element name="same_circularised_filter" file="dataset.same_circularised.filter.sam" lines_diff="8" /> | |
162 <element name="same_internal_filter" file="dataset.same_internal.filter.sam" lines_diff="8" /> | |
163 <element name="filter_piechart" file="filter_piechart.svg" ftype="svg" lines_diff="1000" /> | |
164 | |
165 <!-- deduplicator step--> | |
166 <element name="cis_trans_piechart" file="deduplicator_cis_trans_piechart.svg" ftype="svg" lines_diff="1000"/> | |
167 <element name="uniques_barchart" file="deduplicator_uniques_barchart.svg" ftype="svg" lines_diff="1000"/> | |
168 <element name="hicup_deduplicator_summary" file="hicup_deduplicator_summary.txt" lines_diff="2"/> | |
169 </output_collection> | |
170 </test> | |
171 </tests> | |
172 <help><![CDATA[ | |
173 | |
174 For help please consult the documentation of HiCUP: http://www.bioinformatics.babraham.ac.uk/projects/hicup/overview/ | |
175 | |
176 To get more information about the pipeline visit: http://www.bioinformatics.babraham.ac.uk/projects/hicup/scripts_description/#HiCUP | |
177 ]]></help> | |
178 <expand macro="citation_hicup" /> | |
179 </tool> |