Mercurial > repos > artbio > wisecondorx
comparison wisecondor_npz_converter.xml @ 0:bf0ebc9921f2 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/wisecondorx commit b391b0f3348bd86a5c276dc4d3ff9dc98890c115
| author | artbio |
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| date | Sun, 15 Dec 2024 16:37:13 +0000 |
| parents | |
| children |
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| -1:000000000000 | 0:bf0ebc9921f2 |
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| 1 <tool id="wisecondorx_npz_converter" name="WisecondorX convert" version="@WRAPPER_VERSION@" profile="@PROFILE@"> | |
| 2 <description> | |
| 3 bam to npz | |
| 4 </description> | |
| 5 <macros> | |
| 6 <import>macro.xml</import> | |
| 7 </macros> | |
| 8 <expand macro="requirements"/> | |
| 9 <stdio> | |
| 10 <exit_code range="1:" level="fatal" description="Error occured" /> | |
| 11 </stdio> | |
| 12 <command detect_errors="exit_code"><![CDATA[ | |
| 13 @pipefail@ | |
| 14 ln -f -s $bam.metadata.bam_index input.bam.bai && | |
| 15 ln -f -s $bam input.bam && | |
| 16 printf "Creating 5kb bins for file $bam.element_identifier" && | |
| 17 WisecondorX convert input.bam output.npz | |
| 18 ]]></command> | |
| 19 <inputs> | |
| 20 <param name="bam" type="data" label="Bam input" format="bam" | |
| 21 help="input Bam is converted in .npz file"/> | |
| 22 </inputs> | |
| 23 <outputs> | |
| 24 <data name="npz" format="npz" from_work_dir="output.npz" label="${on_string}.npz" /> | |
| 25 </outputs> | |
| 26 <tests> | |
| 27 <test expect_num_outputs="1"> | |
| 28 <param ftype="bam" name="bam" value="npz_convert_input.bam" /> | |
| 29 <output name="npz" ftype="npz" file="npz_convert_output.npz" compare="sim_size" delta="10000"/> | |
| 30 </test> | |
| 31 </tests> | |
| 32 <help> | |
| 33 @help@ | |
| 34 <![CDATA[ | |
| 35 .. class:: infomark | |
| 36 | |
| 37 **WisecondorX convert input.bam/cram output.npz [--optional arguments]** | |
| 38 | |
| 39 Option List:: | |
| 40 | |
| 41 --reference Fasta reference to be used with cram inputs. | |
| 42 This option is currently not available in this Galaxy wrapper, | |
| 43 which takes only bam inputs. | |
| 44 --binsize Size per bin in bp; the reference bin size should be a multiple of this value. | |
| 45 Note that this parameter does not impact the resolution, yet it | |
| 46 can be used to optimize processing speed (default: x=5e3). | |
| 47 The --binsize parameter is currently not exposed in this Galaxy | |
| 48 wrapper and is fixed to 5e3 | |
| 49 --normdup Use this flag to avoid duplicate removal. | |
| 50 The --normdup parameter is currently not exposed in this Galaxy | |
| 51 wrapper. Default is to remove duplicates. | |
| 52 | |
| 53 ]]></help> | |
| 54 <citations> | |
| 55 <citation type="doi">10.1093/nar/gky1263</citation> | |
| 56 </citations> | |
| 57 </tool> |