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