Mercurial > repos > iuc > cnvkit_segmetrics

annotate segmetrics.xml @ 0:d9cb65e1f756 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
author iuc
date Fri, 29 Sep 2023 15:39:32 +0000
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d9cb65e1f756 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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1 <tool id="cnvkit_segmetrics" name="CNVkit Segmetrics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>calculate summary statistics</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_and_zahra"/>
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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 '$input_filename_file' ./sample.cnr &&
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11 #if $segments
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12 ln -s '$segments' ./sample.cns &&
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13 #end if
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14 cnvkit.py segmetrics
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15 ./sample.cnr
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16 --output gene_segmetrics.cns
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17 #if $segments
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18 --segments ./sample.cns
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19 #end if
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20 $advanced_settings.mean
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21 $advanced_settings.median
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22 $advanced_settings.mode
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23 $advanced_settings.ttest
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24 $advanced_settings.stdev
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25 $advanced_settings.sem
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26 $advanced_settings.mad
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27 $advanced_settings.mse
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28 $advanced_settings.iqr
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29 $advanced_settings.bivar
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30 $advanced_settings.ci
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31 $advanced_settings.pi
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32 $advanced_settings.alpha
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33 $advanced_settings.bootstrap
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34 ]]></command>
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35 <inputs>
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36 <param name="input_filename_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnn/cnr file" help="" />
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37 <param argument="--segments" optional="true" type="data" format="tabular" label="CN segmentation calls cns file" help="" />
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38 <param argument="--drop-low-coverage" type="boolean" checked="false" truevalue="--drop-low-coverage" falsevalue="" label="Drop very-low-coverage bins before segmentation" help="To avoid false-positive deletions in poor-quality tumor samples" />
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39 <section name="advanced_settings" title="Statistical settings" expanded="false">
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40 <expand macro="genemetrics_segmetrics_statistics" />
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41 </section>
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42 </inputs>
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43 <outputs>
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44 <data name="gene_segmetrics" format="tabular" label="${tool.name} on ${on_string}: bin-level log2 ratio" from_work_dir="gene_segmetrics.cns" />
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45 </outputs>
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46 <tests>
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47 <test expect_num_outputs="1">
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48 <param name="input_filename_file" ftype="tabular" value="sample.cnr" />
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49 <param name="segments" ftype="tabular" value="sample.cns" />
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50 <param name="drop_low_coverage" value="1" />
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51 <param name="mean" value="1" />
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52 <param name="median" value="1" />
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53 <param name="mode" value="0" />
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54 <output name="gene_segmetrics">
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55 <assert_contents><has_text text="chromosome"/></assert_contents>
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56 </output>
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57 </test>
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58 </tests>
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59 <help><![CDATA[
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60 Calculate summary statistics of the residual bin-level log2 ratio estimates from the segment means, similar to
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61 the existing metrics command, but for each segment individually. Results are output in the same format as the
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62 CNVkit segmentation file (.cns), with the stat names and calculated values printed in additional columns.
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63 ]]></help>
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64 <expand macro="citations" />
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65 </tool>
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66
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