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