Mercurial > repos > yhoogstrate > segmentation_fold
comparison utils_filter-annotated-entries.xml @ 4:63df1e23f4ff draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 00690c63c51a7f7563f2428c313d7fa75f2657e5-dirty
| author | yhoogstrate |
|---|---|
| date | Thu, 28 Jul 2016 10:25:37 -0400 |
| parents | |
| children | b7cf9b172cfe |
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| 3:cd1bba1c66b3 | 4:63df1e23f4ff |
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| 1 <tool id="smf_utils_filter-annotated-entries" name="filter-annotated-entries" version="@VERSION@-1"> | |
| 2 <description>Split entries into two files based on whether they overlap annotations in a bed file</description> | |
| 3 | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 | |
| 8 <requirements> | |
| 9 <requirement type="package" version="2.7.10">python</requirement> | |
| 10 <requirement type="package" version="1.9">numpy</requirement> | |
| 11 <requirement type="package" version="0.8.2.1">pysam</requirement> | |
| 12 <requirement type="package" version="0.6.1">htseq</requirement> | |
| 13 <requirement type="package" version="2.0.1">segmentation-fold-utils</requirement> | |
| 14 </requirements> | |
| 15 <expand macro="stdio" /> | |
| 16 | |
| 17 <version_command>@VERSION_COMMAND_UTILS@</version_command> | |
| 18 | |
| 19 <command><![CDATA[ | |
| 20 segmentation-fold-utils | |
| 21 filter-annotated-entries | |
| 22 --regex '${regex.replace("'","\\'")}' | |
| 23 '$dbn_input_file' | |
| 24 '$bed_input_file' | |
| 25 '$dbn_output_file_overlapping' | |
| 26 '$dbn_output_file_non_overlapping' | |
| 27 ]]></command> | |
| 28 | |
| 29 <inputs> | |
| 30 <param name="dbn_input_file" | |
| 31 type="data" | |
| 32 format="dbn,txt" | |
| 33 label="Input DBN file" | |
| 34 help="The 'fasta'-headers should contain the genomic position being used to find overlapping reads in the BAM file"/> | |
| 35 <param name="bed_input_file" | |
| 36 type="data" | |
| 37 format="bed" | |
| 38 label="The resultes will be filtered based on overlap with annotations in this BED file"/> | |
| 39 <param name="regex" | |
| 40 type="text" | |
| 41 argument="--regex" | |
| 42 value='>.*?(chr[^:]):([0-9]+)-([0-9]+)' | |
| 43 label="Regex to capture the targeted location in DBN file" | |
| 44 help="Do not change this value unless you're using customized software in the pipeline - default: '>.*?(chr[^:]):([0-9]+)-([0-9]+)'" /> | |
| 45 </inputs> | |
| 46 | |
| 47 <outputs> | |
| 48 <data name="dbn_output_file_overlapping" | |
| 49 format="dbn" | |
| 50 label="${tool.name} on ${dbn_input_file.hid}: ${dbn_input_file.name} - overlapping entries"/> | |
| 51 <data name="dbn_output_file_non_overlapping" | |
| 52 format="dbn" | |
| 53 label="${tool.name} on ${dbn_input_file.hid}: ${dbn_input_file.name} - non overlapping entries"/> | |
| 54 </outputs> | |
| 55 | |
| 56 <tests> | |
| 57 <test> | |
| 58 <param name="dbn_input_file" value="DBNFile.test_02.in.dbn" ftype="dbn"/> | |
| 59 <param name="bed_input_file" value="DBNFile.test_02.in.bed" ftype="bed"/> | |
| 60 <param name="regex" value='>.*?(chr[^:]):([0-9]+)-([0-9]+)'/> | |
| 61 | |
| 62 <output name="dbn_output_file_overlapping"> | |
| 63 <assert_contents> | |
| 64 <has_line_matching expression=">chr1:0-10 x unknown-01 \(overlap in .*?: firstbase,1-2-3-4-5,6-7-8-9-10\)"/> | |
| 65 <has_line line="AAAAAAAAAA"/> | |
| 66 </assert_contents> | |
| 67 </output> | |
| 68 <output name="dbn_output_file_non_overlapping"> | |
| 69 <assert_contents> | |
| 70 <has_line_matching expression=">chr1:25-36 x unknown-01 \(aligned reads .*?: 1\)"/> | |
| 71 <has_line line="AAAAAAAAAAA"/> | |
| 72 | |
| 73 <has_line_matching expression=">chr1:45-56 x unknown-01 \(aligned reads .*?: 2\)"/> | |
| 74 </assert_contents> | |
| 75 </output> | |
| 76 </test> | |
| 77 </tests> | |
| 78 | |
| 79 <help><![CDATA[ | |
| 80 Filter based on whether the entries in the DBN file are already annotated or not | |
| 81 ]]></help> | |
| 82 | |
| 83 <expand macro="citations" /> | |
| 84 </tool> |