Mercurial > repos > iuc > odgi_build

annotate build.xml @ 1:7eb7b43eb912 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit cd3b054df45f2805457941fa09170389f99df80e"
author iuc
date Thu, 09 Apr 2020 06:35:17 +0000
parents 61e02e52ce73
children a0d72fc028e2
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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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1 <tool id="odgi_build" name="odgi build" version="@TOOL_VERSION@">
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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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>
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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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"/>
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7 <command detect_errors="exit_code"><![CDATA[
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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8 odgi build
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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9 -g '$gfa'
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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10 -o '$odgi_output'
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11 $sort
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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12 #if $to_gfa:
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13 --to-gfa > '$gfa_output'
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14 #end if
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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15 ]]></command>
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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16 <inputs>
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17 <param argument="--gfa" type="data" format="gfa1" label="Construct the graph from this GFA input file" />
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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18 <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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19 label="Topological sort the graph"
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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20 help="Apply generalized topological sort to the graph and set node ids to order." />
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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21 <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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22 label="Output additional GFA file"
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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23 help="" />
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24 </inputs>
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25 <outputs>
1
7eb7b43eb912 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit cd3b054df45f2805457941fa09170389f99df80e"
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26 <data name="odgi_output" format="odgi" label="${tool.name} on ${on_string}: odgi" />
7eb7b43eb912 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit cd3b054df45f2805457941fa09170389f99df80e"
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27 <data name="gfa_output" format="gfa1" label="${tool.name} on ${on_string}: GFA">
0
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28 <filter>to_gfa</filter>
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29 </data>
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="gfa" value="t.gfa" />
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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34 <param name="sort" value="true" />
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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35 <param name="to_gfa" value="true" />
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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36 <output name="odgi_output" file="note5_out.og" />
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37 <output name="gfa_output" file="note5.gfa" />
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38 </test>
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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39 </tests>
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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40 <help><![CDATA[
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41 optimized dynamic genome/graph implementation (odgi)
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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42 ----------------------------------------------------
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43
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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44 Construct a dynamic succinct variation graph (build)
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45 ]]></help>
61e02e52ce73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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46 <expand macro="citations">
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47 </expand>
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48 </tool>