Mercurial > repos > iuc > odgi_viz

annotate vis.xml @ 1:b1319597ce74 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 06:35:41 +0000
parents 1b69beb7fb85
children 1e55f76c3b72
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1b69beb7fb85 "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_viz" name="odgi viz" version="@TOOL_VERSION@">
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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2 <description>variation graph visualizations</description>
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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3 <macros>
1b69beb7fb85 "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>
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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5 </macros>
1b69beb7fb85 "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"/>
1b69beb7fb85 "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[
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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8 odgi viz
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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9 -i '$input'
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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10 --out='$output'
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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11 -x $width
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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12 -y $height
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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13 #if str($path_height)
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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14 --path-height=$path_height
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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15 #end if
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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16 #if str($path_x_padding)
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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17 --path-x-padding=$path_x_padding
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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18 #end if
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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19 $path_per_row
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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20 #if str($link_path_pieces):
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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21 --link-path-pieces=$link_path_pieces
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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22 #end if
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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23 --threads=\${GALAXY_SLOTS:-1}
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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24 ]]></command>
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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25 <inputs>
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
iuc
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26 <param name="input" type="data" format="odgi" label="odgi input file" />
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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27
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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28 <param argument="--width" type="integer" min="0" value="4000" label="Width in pixels of output image" />
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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29 <param argument="--height" type="integer" min="0" value="500" label="Height in pixels of output image" />
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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30
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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31 <param argument="--path-height" type="integer" min="0" optional="true" label="Path display height" />
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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32 <param argument="--path-x-padding" type="integer" min="0" optional="true" label="Path x padding" />
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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33 <param argument="--path-per-row" type="boolean" truevalue="--path-per-row" falsevalue=""
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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34 label="Display a single path per row rather than packing them" />
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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35
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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36 <param argument="--link-path-pieces" type="float" optional="true"
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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37 label="Show thin links of this relative width to connect path pieces" />
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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38 </inputs>
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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39 <outputs>
1
b1319597ce74 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit cd3b054df45f2805457941fa09170389f99df80e"
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40 <data name="output" format="png" label="${tool.name} on ${on_string}" />
0
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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41 </outputs>
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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42 <tests>
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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43 <test>
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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44 <param name="input" value="note5_out.og" />
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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45 <param name="width" value="4000" />
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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46 <param name="height" value="500" />
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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47 <output name="output" file="note5.png" ftype="png" />
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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48 </test>
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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49 </tests>
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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50 <help><![CDATA[
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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51 optimized dynamic genome/graph implementation (odgi)
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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52 ----------------------------------------------------
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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53
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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54 variation graph visualizations (viz)
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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55 ]]></help>
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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56 <expand macro="citations" />
1b69beb7fb85 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/odgi/ commit 6de23fe4201ec9c2b209f00ae0e19962c232828c"
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57 </tool>