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comparison VarAmpliCNV_GC.xml @ 1:5c324f9a4e20 draft default tip

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author geert-vandeweyer
date Fri, 25 Sep 2020 08:30:57 +0000
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0:febc6023d37b 1:5c324f9a4e20
1 <tool id="VarAmpliCNV_GC" name="Get Amplicon GC-Content" version="0.1.0" python_template_version="2.7">
2 <requirements>
3 <container type="docker">cmgantwerpen/varamplicnv:1.0.0</container>
4 </requirements>
5 <command detect_errors="exit_code"><![CDATA[
6 getGCAmplicon.py
7
8 ## amplicon input file
9 -a '$input'
10
11 ## output file
12 -o '$gcOut'
13
14 ## 2bit reference gene file
15 -f $index
16
17 ]]></command>
18 <inputs>
19 <param name="input" type="data" format="bed" optional="false" label="Amplicon Design File (BED)" help="This file is the HaloPlex design file, containing individual amplicons." />
20 <param name="index" type="select">
21 <options from_data_table="TwoBitDocker" />
22 </param>
23 </inputs>
24 <outputs>
25 <data name="gcOut" format="tabular" label="VarAmpliCNV on ${on_string}: GC-content" />
26 <!--<data name="ampliconOut" format="tabular" label="Amplicon Gene annotations" />-->
27 </outputs>
28 <help>
29 **VarAmpliCNV : GC-calculation**
30
31 Calculate the GC-content of entries in a BED file.
32
33 **Parameters are :**
34
35 * Amplicon Design File (BED) : The de-duplicated amplicon list, generated by "varAmpliCNV Annotate".
36 * Genome Build : Select a genome build from the configured options to extract GC content from.
37
38 **Output files :**
39
40 * GC-content (txt) : Tabular file containing GC information per region.
41
42 </help>
43 </tool>