Mercurial > repos > bgruening > hicup_hicup_hicup
comparison hicup_macros.xml @ 0:a92f651b9a00 draft default tip
planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit f70ecd67ac0a08e34c2a6c7742fe7ce7d1456630
| author | bgruening |
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| date | Thu, 09 Mar 2017 08:32:15 -0500 |
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| children |
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| -1:000000000000 | 0:a92f651b9a00 |
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| 1 | |
| 2 <macros> | |
| 3 <xml name="requirements_hicup"> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="0.5.9">hicup</requirement> | |
| 6 <requirement type="package" version="2.2.6">bowtie2</requirement> | |
| 7 <requirement type="package" version="1.2">samtools</requirement> | |
| 8 <requirement type="package" version="0.13.1">docutils</requirement> | |
| 9 </requirements> | |
| 10 </xml> | |
| 11 <xml name="stdio"> | |
| 12 <stdio> | |
| 13 <exit_code range="1:" /> | |
| 14 </stdio> | |
| 15 </xml> | |
| 16 <xml name="citation_hicup"> | |
| 17 <citations> | |
| 18 <citation type="doi">10.12688/f1000research.7334.1</citation> | |
| 19 </citations> | |
| 20 </xml> | |
| 21 <xml name="reference_genome_macro"> | |
| 22 <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"> | |
| 24 <option value="indexed">Use a built-in genome index</option> | |
| 25 <option value="history">Use a genome from the history and build index</option> | |
| 26 </param> | |
| 27 <when value="indexed"> | |
| 28 <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team"> | |
| 29 <options from_data_table="bowtie2_indices"> | |
| 30 <filter type="sort_by" column="2"/> | |
| 31 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | |
| 32 </options> | |
| 33 </param> | |
| 34 </when> | |
| 35 <when value="history"> | |
| 36 <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" />--> | |
| 38 </when> | |
| 39 </conditional> | |
| 40 </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 | |
| 66 </xml> | |
| 67 <xml name="input_files"> | |
| 68 <param name="input_first_sequence" type="data" format="fastq" label="First input sequence" help="The first sequence:"/> | |
| 69 <param name="input_second_sequence" type="data" format="fastq" label="Second input sequence" help="The second sequence:"/> | |
| 70 </xml> | |
| 71 <xml name="re1"> | |
| 72 <param argument="--re1" type="text" value="" label="Restriction enzyme recognition sequence" help="Restriction enzyme recognition sequence"/> | |
| 73 </xml> | |
| 74 <xml name="re2"> | |
| 75 <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."/> | |
| 76 </xml> | |
| 77 <xml name="digester_input"> | |
| 78 <param name="input_files_digest" type="data" multiple="true" format="fa" label="Input DNA sequence files that should be digested"/> | |
| 79 <param argument="--genome" type="text" label="Genome" help="Name of the genome to be digested (not the path to the genome | |
| 80 file or files, but the genome name to include in the output file)"/> | |
| 81 </xml> | |
| 82 <xml name="filter_longest_shortest"> | |
| 83 <param argument="--longest" type="text" value="" label="Max insert size" help="Maximum allowable insert size (bps)"/> | |
| 84 <param argument="--shortest" type="text" value="" label="Min insert size" help="Minimum allowable insert size (bps)"/> | |
| 85 </xml> | |
| 86 <xml name="no_fill"> | |
| 87 <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"/> | |
| 88 </xml> | |
| 89 <xml name="deduplicator_output"> | |
| 90 <data name="cis_trans_piechart" format="svg" from_work_dir="deduplicator_cis_trans_piechart.svg" label="Hicup Deduplicator Cis Trans Piechart.svg"/> | |
| 91 <data name="uniques_barchart" format="svg" from_work_dir="deduplicator_uniques_barchart.svg" label="Hicup Deduplicator Uniques Barchart.svg" /> | |
| 92 <data name="hicup_deduplicator_summary" format="txt" from_work_dir="hicup_deduplicator_summary.txt" label="Hicup Deduplicator Summary" /> | |
| 93 </xml> | |
| 94 </macros> |