comparison sex.xml @ 0:3316bd294f6f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
author iuc
date Fri, 29 Sep 2023 15:44:27 +0000
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-1:000000000000 0:3316bd294f6f
1 <tool id="cnvkit_sex" name="CNVkit Sex" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
2 <description>Guess samples’ chromosomal sex from the relative coverage of chromosomes X and Y</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 cnvkit.py sex
12 ./sample.cnr
13 --output gene-sex.txt
14 $male_reference
15 ]]></command>
16 <inputs>
17 <param name="input_filename_file" type="data" format="tabular" label="Bin-Level log2 Ratios/Coverages cnr/cnn file" help="Copy number cnn or copy ratio cnr files" />
18 <param argument="--male-reference" type="boolean" checked="false" truevalue="--male-reference" falsevalue="" label="MALE REFERENCE" help="Assume inputs were normalized to a male reference" />
19 </inputs>
20 <outputs>
21 <data name="gene_sex" format="txt" label="${tool.name} on ${on_string}: sample's chromosomal sex" from_work_dir="gene-sex.txt" />
22 </outputs>
23 <tests>
24 <test expect_num_outputs="1">
25 <param name="input_filename_file" ftype="tabular" value="sample.cnr" />
26 <output name="gene_sex" file="gene-sex.txt" />
27 </test>
28 </tests>
29 <help><![CDATA[
30 Guess samples’ chromosomal sex from the relative coverage of chromosomes X and Y.
31 The output is a table of the sample name (derived from the filename), inferred sex (string “Female” or “Male”),
32 and log2 ratio value of chromosomes X and Y.
33 ]]></help>
34 <expand macro="citations" />
35 </tool>
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