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annotate fix.xml @ 0:f64acbe71392 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
author iuc
date Sun, 14 May 2023 20:11:33 +0000
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f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
iuc
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1 <tool id="cnvkit_fix" name="CNVkit Fix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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2 <description>Adjust raw coverage data</description>
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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3 <macros>
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4 <import>macros.xml</import>
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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5 </macros>
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ln -s '$input_target_file' ./tumor.targetcoverage.cnn &&
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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10 #if $input_antitarget_file
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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11 ln -s '$input_antitarget_file' ./tumor.antitargetcoverage.cnn &&
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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12 #end if
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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13 #if $input_reference_coverage_file
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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14 ln -s '$input_reference_coverage_file' ./ref-tas.cnn &&
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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15 #end if
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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16 cnvkit.py fix
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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17 ./tumor.targetcoverage.cnn
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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18 #if $input_antitarget_file
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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19 ./tumor.antitargetcoverage.cnn
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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20 #end if
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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21 #if $input_reference_coverage_file
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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22 ./ref-tas.cnn
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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23 #end if
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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24 --output sample.cnr
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25 $cluster
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26 #if $sample_id
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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27 --sample-id '$sample_id'
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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28 #end if
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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29 $no_gc
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30 $no_edge
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31 $no_rmask
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32 ]]></command>
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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33 <inputs>
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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34 <param name="input_target_file" type="data" format="bam" label="Target coverage file" help="" />
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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35 <param name="input_antitarget_file" type="data" optional="true" format="tabular" label="Antitarget coverage file" help="" />
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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36 <param name="input_reference_coverage_file" type="data" optional="true" format="tabular" label="Reference coverage" help="" />
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37 <param argument="--cluster" type="boolean" checked="false" truevalue="--cluster" falsevalue="" label="Compare and use cluster-specific values present in the reference profile" help="" />
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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38 <param argument="--sample-id" optional="true" type="text" label="Sample ID for target/antitarget files" value="" help="Otherwise inferred from file names" />
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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39 <param argument="--no-gc" type="boolean" checked="false" truevalue="--no-gc" falsevalue="" label="Skip GC correction" help="" />
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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40 <param argument="--no-edge" type="boolean" checked="false" truevalue="--no-edge" falsevalue="" label="Skip edge-effect correction" help="" />
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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41 <param argument="--no-rmask" type="boolean" checked="false" truevalue="--no-rmask" falsevalue="" label=" Skip RepeatMasker correction" help="" />
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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42 </inputs>
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43 <outputs>
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44 <data name="out_sample_cnr" format="tabular" label="${tool.name} on ${on_string}: Sample copy number ratios table" from_work_dir="sample.cnr" />
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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_target_file" ftype="tabular" value="tumor.targetcoverage.cnn" />
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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49 <param name="input_antitarget_file" ftype="tabular" value="tumor.antitargetcoverage.cnn" />
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50 <param name="input_reference_coverage_file" ftype="tabular" value="ref-tas.cnn" />
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51 <param name="no_edge" value="1" />
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52 <output name="out_sample_cnr">
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53 <assert_contents><has_text text="chromosome"/></assert_contents>
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54 </output>
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58 Combine the uncorrected target and antitarget coverage tables (.cnn) and correct for biases
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59 in regional coverage and GC content, according to the given reference.
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60
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61 The reference .cnn file output contains those columns
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62 chromosome, Start, end, gene, GC content of the sequence region (gc), RepeatMasker-masked proportion
f64acbe71392 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit c35b83e4b65b211377c9f616c77d7306da48a984
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63 of the sequence region (rmask), Statistical spread or dispersion (spread), Robust average of coverage
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64 depths (log2 ) and Robust average of absolute-scale coverage depths without any bias corrections (depth)
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65 ]]></help>
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66 <expand macro="citations" />
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67 </tool>