Mercurial > repos > bgruening > hicup_deduplicator

comparison hicup_macros.xml @ 4:46e5b4782715 draft

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planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit 22eec1b3b20b788e762837c02488f332f831fab3
author bgruening
date Fri, 25 May 2018 17:51:57 -0400
parents 6551ad3d75f4
children a5934ac7c399
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3:6551ad3d75f4 4:46e5b4782715
1 <macros> 1 <macros>
2 <token name="@VERSION@">0.5.10</token> 2 <token name="@VERSION@">0.6.1</token>
3 <xml name="requirements_hicup"> 3 <xml name="requirements_hicup">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="@VERSION@">hicup</requirement> 5 <requirement type="package" version="@VERSION@">hicup</requirement>
6 <requirement type="package" version="2.2.6">bowtie2</requirement> 6 <requirement type="package" version="2.2.6">bowtie2</requirement>
7 <requirement type="package" version="1.2">samtools</requirement> 7 <requirement type="package" version="1.2">samtools</requirement>
8 <requirement type="package" version="0.13.1">docutils</requirement> 8 <requirement type="package" version="0.13.1">docutils</requirement>
9 <yield/>
9 </requirements> 10 </requirements>
10 </xml> 11 <version_command>hicup --version</version_command>
11 <xml name="stdio">
12 <stdio>
13 <exit_code range="1:" />
14 </stdio>
15 </xml> 12 </xml>
16 <xml name="citation_hicup"> 13 <xml name="citation_hicup">
17 <citations> 14 <citations>
18 <citation type="doi">10.12688/f1000research.7334.1</citation> 15 <citation type="doi">10.12688/f1000research.7334.1</citation>
19 </citations> 16 </citations>
20 </xml> 17 </xml>
21 <xml name="reference_genome_macro"> 18 <xml name="reference_genome_macro">
22 <conditional name="reference_genome"> 19 <conditional name="reference_genome">
23 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below"> 20 <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
24 <option value="indexed">Use a built-in genome index</option> 21 <option value="indexed">Use a built-in genome index</option>
36 <param name="own_file" type="data" format="fasta" label="Select reference genome" /> 33 <param name="own_file" type="data" format="fasta" label="Select reference genome" />
37 <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />--> 34 <!--<param name="own_file" type="data" format="fasta" metadata_name="dbkey" label="Select reference genome" />-->
38 </when> 35 </when>
39 </conditional> 36 </conditional>
40 </xml> 37 </xml>
41 <xml name="filter_output">
42 <data name="dataset_filt" format="sam" from_work_dir="dataset.filt.sam" label="filt.sam" />
43 <data name="hicup_filter_summary" format="txt" from_work_dir="hicup_filter_summary.txt" label="hicup_filter_summary.txt" />
44 <data name="contiguous_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.contiguous.filter.sam" label="contiguous.filter.sam" />
45 <data name="re_ligation_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.re_ligation.filter.sam" label="re_ligation.filter.sam" />
46 <data name="same_dangling_ends_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_dangling_ends.filter.sam" label="same_dangling_ends.filter.sam" />
47 <data name="invalid_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.invalid.filter.sam" label="invalid.filter.sam" />
48 <data name="same_circularised_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_circularised.filter.sam" label="same_circularised.filter.sam" />
49 <data name="same_internal_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.same_internal.filter.sam" label="same_internal.filter.sam" />
50 <data name="wrong_size_filter" format="sam" from_work_dir="hicup_filter_ditag_rejects/dataset.wrong_size.filter.sam" label="wrong_size.filter.sam"/>
51 <data name="filter_piechart" format="svg" from_work_dir="filter_piechart.svg" label="Filter piechart.svg" />
52 </xml>
53 <xml name="mapper_output">
54 <data name="hicup_mapper_summary" format="txt" from_work_dir="hicup_mapper_summary.txt" label="hicup_mapper_summary.txt"/>
55 <data name="result_pair" format="sam" from_work_dir="result.pair.sam" label="pair.sam"/>
56 <data name="dataset1_mapper_barchart" format="svg" from_work_dir="dataset1.mapper_barchart.svg" label="Mapper Dataset1 Barchart.svg" />
57 <data name="dataset2_mapper_barchart" format="svg" from_work_dir="dataset2.mapper_barchart.svg" label="Mapper Dataset2 Barchart.svg" />
58 </xml>
59 <xml name="truncater_output">
60 <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary.txt" />
61 <data name="dataset1_trunc" format="fastq" label="Hicup Dataset1 Truncation" from_work_dir="dataset1.trunc.fastq" />
62 <data name="dataset2_trunc" format="fastq" label="Hicup Dataset2 Truncation" from_work_dir="dataset2.trunc.fastq" />
63 <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1.truncation_barchart.svg" />
64 <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2.truncation_barchart.svg" />
65 </xml>
66 <xml name="input_files"> 38 <xml name="input_files">
67 <param name="input_first_sequence" type="data" format="fastq" label="First input sequence" help="The first sequence:"/> 39 <param name="input_first_sequence" type="data" format="fastq,fastq.gz" label="First input sequence" help="The first sequence:"/>
68 <param name="input_second_sequence" type="data" format="fastq" label="Second input sequence" help="The second sequence:"/> 40 <param name="input_second_sequence" type="data" format="fastq,fastq.gz" label="Second input sequence" help="The second sequence:"/>
69 </xml> 41 </xml>
70 <xml name="re1"> 42 <xml name="re1">
71 <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme recognition sequence"/> 43 <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme recognition sequence"/>
72 </xml> 44 </xml>
73 <xml name="re2"> 45 <xml name="re2">
74 <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags." help="To specify a restriction enzyme instead of sonication to shorten di-tags. This restriction site does NOT form a Hi-C ligation junction. 2 .g. AG^CT,AluI. Typically the sonication protocol is followed."/> 46 <param argument="--re2" type="text" value="" label="Restriction enzyme instead of sonication to shorten di-tags."
75 </xml> 47 help="To specify a restriction enzyme instead of sonication to shorten di-tags. This restriction site does NOT form a Hi-C ligation junction. 2 .g. AG^CT,AluI. Typically the sonication protocol is followed."/>
76 <xml name="digester_input">
77 <param name="input_files_digest" type="data" multiple="true" format="fasta" label="Input DNA sequence files that should be digested"/>
78 <param argument="--genome" type="text" label="Genome" help="Name of the genome to be digested (not the path to the genome
79 file or files, but the genome name to include in the output file)"/>
80 </xml> 48 </xml>
81 <xml name="filter_longest_shortest"> 49 <xml name="filter_longest_shortest">
82 <param argument="--longest" type="text" value="" label="Max insert size" help="Maximum allowable insert size (bps)"/> 50 <param argument="--longest" type="text" value="" label="Max insert size" help="Maximum allowable insert size (bps)"/>
83 <param argument="--shortest" type="text" value="" label="Min insert size" help="Minimum allowable insert size (bps)"/> 51 <param argument="--shortest" type="text" value="" label="Min insert size" help="Minimum allowable insert size (bps)"/>
84 </xml> 52 </xml>
85 <xml name="no_fill"> 53 <xml name="no_fill">
86 <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill" help="Hi-C protocol did NOT include a fill-in of sticky ends prior to re-ligation and therefore reads shall be truncated at the restriction site sequence"/> 54 <param argument="--nofill" type="boolean" value="false" truevalue="--nofill" falsevalue="" label="No fill"
87 </xml> 55 help="Hi-C protocol did NOT include a fill-in of sticky ends prior to re-ligation and therefore reads shall be truncated at the restriction site sequence"/>
88 <xml name="deduplicator_output">
89 <data name="cis_trans_piechart" format="svg" from_work_dir="deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/>
90 <data name="uniques_barchart" format="svg" from_work_dir="deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" />
91 <data name="hicup_deduplicator_summary" format="txt" from_work_dir="hicup_deduplicator_summary.txt" label="Hicup Deduplicator Summary" />
92 </xml> 56 </xml>
93 </macros> 57 </macros>