Mercurial > repos > iuc > odgi_build
annotate build.xml @ 0:0acf4893bee5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
author | iuc |
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date | Wed, 08 Apr 2020 12:12:18 -0400 |
parents | |
children | 7fb3bb1e221e |
rev | line source |
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0
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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1 <tool id="odgi_build" name="odgi build" version="@TOOL_VERSION@"> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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2 <description>construct a dynamic succinct variation graph</description> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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3 <macros> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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4 <import>macros.xml</import> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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5 </macros> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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6 <expand macro="requirements"/> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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7 <command detect_errors="exit_code"><![CDATA[ |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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8 odgi build |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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9 -g '$gfa' |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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10 -o '$odgi_output' |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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11 $sort |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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12 #if $to_gfa: |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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13 --to-gfa > '$gfa_output' |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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14 #end if |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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15 ]]></command> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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16 <inputs> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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17 <param argument="--gfa" type="data" format="gfa1" label="Construct the graph from this GFA input file" /> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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18 <param argument="--sort" type="boolean" truevalue="--sort" falsevalue="" checked="false" |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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19 label="Topological sort the graph" |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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20 help="Apply generalized topological sort to the graph and set node ids to order." /> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
diff
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21 <param argument="--to-gfa" type="boolean" truevalue="--to-gfa" falsevalue="" checked="false" |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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22 label="Output additional GFA file" |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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23 help="" /> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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24 </inputs> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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25 <outputs> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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26 <data name="odgi_output" format="odgi" /> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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27 <data name="gfa_output" format="gfa1"> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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28 <filter>to_gfa</filter> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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29 </data> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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30 </outputs> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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31 <tests> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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32 <test> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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33 <param name="gfa" value="t.gfa" /> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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34 <param name="sort" value="true" /> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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35 <param name="to_gfa" value="true" /> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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36 <output name="odgi_output" file="note5_out.og" /> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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37 <output name="gfa_output" file="note5.gfa" /> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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38 </test> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
parents:
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39 </tests> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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40 <help><![CDATA[ |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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41 optimized dynamic genome/graph implementation (odgi) |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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42 ---------------------------------------------------- |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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43 |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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44 Construct a dynamic succinct variation graph (build) |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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45 ]]></help> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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46 <expand macro="citations"> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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47 </expand> |
0acf4893bee5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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48 </tool> |