Mercurial > repos > artbio > wisecondorx

comparison wisecondor_reference_builder.xml @ 0:bf0ebc9921f2 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/wisecondorx commit b391b0f3348bd86a5c276dc4d3ff9dc98890c115
author artbio
date Sun, 15 Dec 2024 16:37:13 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:bf0ebc9921f2
1 <tool id="wisecondorx_reference_builder" name="WisecondorX build" version="@WRAPPER_VERSION@" profile="@PROFILE@">
2 <description>
3 reference
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 #for $num, $file in enumerate($npz_inputs):
15 ln -s $file "${num}.npz" &&
16 #end for
17 WisecondorX newref *.npz reference.npz
18 --binsize ${bin}
19 --cpus \${GALAXY_SLOTS:-4} &&
20 mv reference.npz $npz
21 ]]></command>
22 <inputs>
23 <param name="npz_inputs" type="data" label="npz inputs" multiple="True" format="npz"
24 help="Build reference from npz inputs from normal sample (at least 10 samples required)"/>
25 <param name="bin" size="9" type="integer" value="100000" label="Bin size in nucleotides"
26 help="Bin default value is 100 kb (100000)" />
27 </inputs>
28 <outputs>
29 <data name="npz" format="npz" label="reference_${bin}nt" />
30 </outputs>
31 <tests>
32 <test expect_num_outputs="1">
33 <param name="npz_inputs"
34 value="0.ref.npz,1.ref.npz,2.ref.npz,3.ref.npz,4.ref.npz,5.ref.npz,6.ref.npz,7.ref.npz,8.ref.npz,9.ref.npz"/>
35 <param name="bin" value="10000" />
36 <output name="npz" ftype="npz" file="output_reference.npz" compare="sim_size" delta="10000"/>
37 </test>
38 </tests>
39 <help>
40 @help@
41 <![CDATA[
42 .. class:: infomark
43
44 **WisecondorX newref reference_input_dir/*.npz reference_output.npz [--optional arguments]**
45
46 Option List::
47
48 --nipt Always include this flag for the generation of a NIPT reference
49 --binsize Size per bin in bp, defines the resolution of the output (default: x=1e5)
50 **Should be a multiple of the 5e3**
51 --refsize Amount of reference locations per target;
52 should generally not be tweaked (default: x=300)
53 --yfrac Y read fraction cutoff, in order to manually define gender.
54 Setting this to 1 will treat all samples as female.
55 This parameter is not currently exposed in the Galaxy wrapper.
56 --plotyfrac plots Y read fraction histogram and Gaussian mixture fit to file x,
57 can help when setting --yfrac manually; software quits after plotting
58 The --normdup parameter is currently not exposed in this Galaxy
59 wrapper. Default is to remove duplicates.
60 --cpus Number of threads requested (This is defined by the Galaxy administrator)
61
62 ]]></help>
63 <citations>
64 <citation type="doi">10.1093/nar/gky1263</citation>
65 </citations>
66 </tool>