Mercurial > repos > iuc > vg_convert

annotate convert.xml @ 0:e68d9dfa62a2 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
author iuc
date Thu, 09 Apr 2020 04:35:27 -0400
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children 7366704232b6
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e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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1 <tool id="vg_convert" name="vg convert" version="@TOOL_VERSION@">
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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2 <description></description>
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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3 <macros>
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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4 <import>macros.xml</import>
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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5 </macros>
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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6 <expand macro="requirements"/>
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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7 <command detect_errors="exit_code"><![CDATA[
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8 ln -s '$infile' ./infile.${infile.ext} &&
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9
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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10 vg convert
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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11 $output_format
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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12 ./infile.${infile.ext}
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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13 > '$output'
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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14 ]]></command>
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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15 <inputs>
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16 <param name="infile" type="data" format="vg,xg" label="Input file in vg or xg format" />
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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17 <param name="output_format" type="select" label="Choose your output format">
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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18 <option value="--xg-out">XG format (--xg-out)</option>
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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19 <!--option value="- -odgi-out">odgi format (- -odgi-out)</option-->
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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20 </param>
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21 </inputs>
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22 <outputs>
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23 <data name="output" format="odgi">
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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24 <change_format>
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25 <when input="output_format" value="--xg-out" format="xg"/>
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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26 </change_format>
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27 </data>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="infile" value="hla.vg" ftype="vg" />
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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32 <param name="output_format" value="--xg-out" />
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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33 <output name="output" file="hla.xg" ftype="xg" compare="sim_size" />
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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34 </test>
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35 <!--test>
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36 <param name="infile" value="x.vg" ftype="vg" />
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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37 <param name="output_format" value="- -odgi-out" />
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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38 <output name="output" file="x.odgi" ftype="odgi" compare="sim_size" />
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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39 </test-->
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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40 </tests>
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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41 <help><![CDATA[
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42
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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43 variation graph (vg) convert module
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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44 -----------------------------------
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45
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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46 This module is converting various variant graphs into each format.
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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47
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48 ]]></help>
e68d9dfa62a2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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49 <expand macro="citations" />
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50 </tool>