Mercurial > repos > iuc > cnvkit_segment

annotate segment.xml @ 2:e1b32558547b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit bced16a45d19b243a244a093c3b3504b2640d5e0
author iuc
date Mon, 22 Apr 2024 17:44:27 +0000
parents c4a22d0fdba5
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9d9a8f230a2f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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1 <tool id="cnvkit_segment" name="CNVkit Segment" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>Infer copy number segments from the given coverage table</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="creators"/>
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8 <expand macro="requirements"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 ln -s '$filename' ./tumor.cnr &&
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11 #if $additional_SNP_allelic_process.vcf
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12 ln -s '$additional_SNP_allelic_process.vcf' ./vcf_file.vcf &&
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13 #end if
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14 #import os
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15 cnvkit.py segment
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16 ./tumor.cnr
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17 --output sample.cns
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18 --processes \${GALAXY_SLOTS:-4}
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19 #if $advanced_settings.dataframe
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20 --dataframe '$advanced_settings.dataframe'
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21 #end if
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22 #if $advanced_settings.method == "cbs"
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23 #set $method_val = "cbs"
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24 --method '$method_val'
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25 #else
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26 --method '$advanced_settings.method'
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27 #end if
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28 #if str($advanced_settings.threshold)
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29 --threshold $advanced_settings.threshold
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30 #end if
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31 $advanced_settings.drop_low_coverage
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32 #if str($advanced_settings.drop_outliers)
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33 --drop-outliers $advanced_settings.drop_outliers
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34 #end if
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35 $advanced_settings.smooth_cbs
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36 #if $additional_SNP_allelic_process.vcf
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37 --vcf ./vcf_file.vcf
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38 #end if
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39 #if $additional_SNP_allelic_process.sample_id
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40 --sample-id '$additional_SNP_allelic_process.sample_id'
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41 #end if
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42 #if $additional_SNP_allelic_process.normal_id
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43 --normal-id '$additional_SNP_allelic_process.normal_id'
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44 #end if
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45 #if str($additional_SNP_allelic_process.min_variant_depth)
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46 --min-variant-depth $additional_SNP_allelic_process.min_variant_depth
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47 #end if
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48 #if str($additional_SNP_allelic_process.zygosity_freq)
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49 --zygosity-freq $additional_SNP_allelic_process.zygosity_freq
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50 #end if
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51 ]]></command>
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52 <inputs>
1
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53 <param name="filename" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr file" help="Use the output of the CNVkit fix" />
0
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54 <section name="additional_SNP_allelic_process" title="additional process for SNP b_allele frequencies" expanded="false">
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55 <expand macro="additionally_SNP_process" />
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56 </section>
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57 <section name="advanced_settings" title="Advanced settings" expanded="false">
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58 <expand macro="segment_optional" />
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59 </section>
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60 </inputs>
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61 <outputs>
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62 <data name="out_sample_segment" format="tabular" label="${tool.name} on ${on_string}: Sample segment" from_work_dir="sample.cns" />
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63 </outputs>
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64 <tests>
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65 <test expect_num_outputs="1">
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66 <param name="filename" ftype="tabular" value="tumor.cnr" />
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67 <param name="method" value="hmm" />
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68 <param name="threshold" value="2" />
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69 <param name="drop_outliers" value="2" />
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70 <param name="drop_low_coverage" value="1" />
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71 <output name="out_sample_segment">
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72 <assert_contents><has_text text="chromosome"/></assert_contents>
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73 </output>
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74 </test>
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75 </tests>
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76 <help><![CDATA[
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77 Infer copy number segments from the given coverage table. Segmentation runs independently on
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78 each chromosome arm, and can be parallelized with the processes option (except for the HMM methods), similar to batch
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79
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80 Segmented log2 ratios (.cns) output file contains those columns
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81 chromosome, Start, end, gene, log2, depth, weight and number of bins covered by the segment (probes)
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82 ]]></help>
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83 <expand macro="citations" />
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84 </tool>