Mercurial > repos > iuc > cnvkit_segmetrics

comparison segmetrics.xml @ 0:d9cb65e1f756 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:d9cb65e1f756
1 <tool id="cnvkit_segmetrics" name="CNVkit Segmetrics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>calculate summary statistics</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="xrefs"/>
7 <expand macro="creators_and_zahra"/>
8 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[
10 ln -s '$input_filename_file' ./sample.cnr &&
11 #if $segments
12 ln -s '$segments' ./sample.cns &&
13 #end if
14 cnvkit.py segmetrics
15 ./sample.cnr
16 --output gene_segmetrics.cns
17 #if $segments
18 --segments ./sample.cns
19 #end if
20 $advanced_settings.mean
21 $advanced_settings.median
22 $advanced_settings.mode
23 $advanced_settings.ttest
24 $advanced_settings.stdev
25 $advanced_settings.sem
26 $advanced_settings.mad
27 $advanced_settings.mse
28 $advanced_settings.iqr
29 $advanced_settings.bivar
30 $advanced_settings.ci
31 $advanced_settings.pi
32 $advanced_settings.alpha
33 $advanced_settings.bootstrap
34 ]]></command>
35 <inputs>
36 <param name="input_filename_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnn/cnr file" help="" />
37 <param argument="--segments" optional="true" type="data" format="tabular" label="CN segmentation calls cns file" help="" />
38 <param argument="--drop-low-coverage" type="boolean" checked="false" truevalue="--drop-low-coverage" falsevalue="" label="Drop very-low-coverage bins before segmentation" help="To avoid false-positive deletions in poor-quality tumor samples" />
39 <section name="advanced_settings" title="Statistical settings" expanded="false">
40 <expand macro="genemetrics_segmetrics_statistics" />
41 </section>
42 </inputs>
43 <outputs>
44 <data name="gene_segmetrics" format="tabular" label="${tool.name} on ${on_string}: bin-level log2 ratio" from_work_dir="gene_segmetrics.cns" />
45 </outputs>
46 <tests>
47 <test expect_num_outputs="1">
48 <param name="input_filename_file" ftype="tabular" value="sample.cnr" />
49 <param name="segments" ftype="tabular" value="sample.cns" />
50 <param name="drop_low_coverage" value="1" />
51 <param name="mean" value="1" />
52 <param name="median" value="1" />
53 <param name="mode" value="0" />
54 <output name="gene_segmetrics">
55 <assert_contents><has_text text="chromosome"/></assert_contents>
56 </output>
57 </test>
58 </tests>
59 <help><![CDATA[
60 Calculate summary statistics of the residual bin-level log2 ratio estimates from the segment means, similar to
61 the existing metrics command, but for each segment individually. Results are output in the same format as the
62 CNVkit segmentation file (.cns), with the stat names and calculated values printed in additional columns.
63 ]]></help>
64 <expand macro="citations" />
65 </tool>
66
67
68
69