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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 7704c7c172c1c511dc23a3e5babdf3bf8e5198eb
author iuc
date Wed, 07 Sep 2022 16:58:30 +0000
parents 7eb7b43eb912
children
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a0d72fc028e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 7704c7c172c1c511dc23a3e5babdf3bf8e5198eb
iuc
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1 <tool id="odgi_build" name="odgi build" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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2 <description>construct a dynamic succinct variation graph</description>
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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6 <expand macro="requirements"/>
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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7 <command detect_errors="exit_code"><![CDATA[
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a0d72fc028e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 7704c7c172c1c511dc23a3e5babdf3bf8e5198eb
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8 cp '$gfa' input.gfa &&
a0d72fc028e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 7704c7c172c1c511dc23a3e5babdf3bf8e5198eb
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9
0
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10 odgi build
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a0d72fc028e2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 7704c7c172c1c511dc23a3e5babdf3bf8e5198eb
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11 -g input.gfa
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61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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12 -o '$odgi_output'
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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13 $sort
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14 #if $to_gfa:
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15 --to-gfa > '$gfa_output'
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16 #end if
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17 ]]></command>
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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18 <inputs>
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19 <param argument="--gfa" type="data" format="gfa1" label="Construct the graph from this GFA input file" />
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20 <param argument="--sort" type="boolean" truevalue="--sort" falsevalue="" checked="false"
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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21 label="Topological sort the graph"
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22 help="Apply generalized topological sort to the graph and set node ids to order." />
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23 <param argument="--to-gfa" type="boolean" truevalue="--to-gfa" falsevalue="" checked="false"
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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24 label="Output additional GFA file"
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25 help="" />
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26 </inputs>
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27 <outputs>
1
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28 <data name="odgi_output" format="odgi" label="${tool.name} on ${on_string}: odgi" />
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29 <data name="gfa_output" format="gfa1" label="${tool.name} on ${on_string}: GFA">
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30 <filter>to_gfa</filter>
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31 </data>
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="gfa" value="t.gfa" />
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36 <param name="sort" value="true" />
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37 <param name="to_gfa" value="true" />
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38 <output name="odgi_output" file="note5_out.og" />
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39 <output name="gfa_output" file="note5.gfa" />
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40 </test>
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41 </tests>
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42 <help><![CDATA[
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43 optimized dynamic genome/graph implementation (odgi)
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44 ----------------------------------------------------
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45
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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46 Construct a dynamic succinct variation graph (build)
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47 ]]></help>
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48 <expand macro="citations">
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49 </expand>
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50 </tool>