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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit 0a6ad31f5095ddf859a4d1819fce5d347f13c462"
author iuc
date Wed, 18 Nov 2020 19:38:38 +0000
parents 28f82ad25daa
children
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28f82ad25daa "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@">
28f82ad25daa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
28f82ad25daa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
1
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8 export TMPDIR=\${TMPDIR:-.};
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9 ln -s '$infile' ./infile.${infile.ext} &&
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10
28f82ad25daa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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11 vg convert
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12 $output_format
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13 ./infile.${infile.ext}
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14 > '$output'
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15 ]]></command>
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16 <inputs>
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17 <param name="infile" type="data" format="vg,xg" label="Input file in vg or xg format" />
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18 <param name="output_format" type="select" label="Choose your output format">
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19 <option value="--xg-out">XG format (--xg-out)</option>
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20 <!--option value="- -odgi-out">odgi format (- -odgi-out)</option-->
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21 </param>
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22 </inputs>
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23 <outputs>
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24 <data name="output" format="odgi">
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25 <change_format>
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26 <when input="output_format" value="--xg-out" format="xg"/>
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27 </change_format>
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28 </data>
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="infile" value="hla.vg" ftype="vg" />
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33 <param name="output_format" value="--xg-out" />
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34 <output name="output" file="hla.xg" ftype="xg" compare="sim_size" />
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35 </test>
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36 <!--test>
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37 <param name="infile" value="x.vg" ftype="vg" />
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38 <param name="output_format" value="- -odgi-out" />
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39 <output name="output" file="x.odgi" ftype="odgi" compare="sim_size" />
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40 </test-->
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41 </tests>
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42 <help><![CDATA[
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43
28f82ad25daa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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44 variation graph (vg) convert module
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45 -----------------------------------
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46
28f82ad25daa "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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47 This module is converting various variant graphs into each format.
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48
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49 ]]></help>
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50 <expand macro="citations" />
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51 </tool>