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comparison egapx_runner.xml @ 1:c8e1543546f8 draft

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planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4-dirty
author fubar
date Sat, 03 Aug 2024 12:10:13 +0000
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0:d9c5c5b87fec 1:c8e1543546f8
1 <tool name="egapx_runner" id="egapx_runner" version="6.0.1" profile="22.05">
2 <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
3 <!--Created by toolfactory@galaxy.org at 03/08/2024 10:40:32 using the Galaxy Tool Factory.-->
4 <description>Runs egapx</description>
5 <requirements>
6 <requirement version="3.12.3" type="package">python</requirement>
7 <requirement version="24.04.4-0" type="package">nextflow</requirement>
8 <requirement version="6.0.1" type="package">pyyaml</requirement>
9 </requirements>
10 <version_command><![CDATA[echo "6.0.1"]]></version_command>
11 <command><![CDATA[mkdir -p ./egapx_config &&
12 #set econfigfile = $econfig + '.config'
13 cp '$__tool_directory__/ui/assets/config/executor/$econfigfile' ./egapx_config/ &&
14 python '$__tool_directory__/ui/egapx.py' '$yamlconfig' -e '$econfig' -o 'egapx_out']]></command>
15 <inputs>
16 <param name="yamlconfig" type="data" optional="false" label="egapx configuration yaml file to execute" help="" format="yaml,txt" multiple="false"/>
17 <param name="econfig" type="select" label="Configuration" help="">
18 <option value="docker_minimal">docker minimal only works for the minimal dust mite sample using 6GB and 4 cores</option>
19 <option value="singularity">singularity requires at least 128GB ram and 32 cores. 256GB and 64 cores recommendd</option>
20 <option value="docker">docker requires at least 128GB ram and 32 cores. 256GB and 64 cores recommend</option>
21 </param>
22 </inputs>
23 <outputs>
24 <collection name="egapx_out" type="list" label="Outputs from egapx">
25 <discover_datasets pattern="__name_and_ext__" directory="egapx_out" visible="false"/>
26 </collection>
27 </outputs>
28
29
30 <tests>
31 <test>
32 <output_collection name="egapx_out" count="8"/>
33 <param name="yamlconfig" value="yamlconfig_sample"/>
34 <param name="econfig" value="docker_minimal"/>
35 </test>
36 </tests>
37
38
39
40 <help><![CDATA[
41 **What it Does**
42 ]]></help>
43 <citations>
44 <citation type="doi">10.1093/bioinformatics/bts573</citation>
45 </citations>
46 </tool>
47