Mercurial > repos > iuc > vg_deconstruct

annotate deconstruct.xml @ 0:a347dad1f305 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 04:36:41 -0400
parents
children 76d18b1e970b
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
iuc
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1 <tool id="vg_deconstruct" name="vg deconstruct" version="@TOOL_VERSION@">
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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2 <description>construct a dynamic succinct variation graph</description>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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3 <macros>
a347dad1f305 "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>
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5 </macros>
a347dad1f305 "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[
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8 ln -s '$infile' ./infile.${infile.ext} &&
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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9
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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10 vg deconstruct
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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11 #if $path:
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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12 --path '${','.join([$p for $p in $path])}'
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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13 #end if
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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14 #if $path_prefix
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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15 --path-prefix '${','.join([$p for $p in $path_prefix])}'
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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16 #end if
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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17 #if $alt_prefix
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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18 --alt-prefix '${','.join([$p for $p in $alt_prefix])}'
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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19 #end if
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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20 #if $snarls:
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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21 --snarls '$snarls'
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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22 #end if
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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23 $path_traversals ## -e
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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24 --threads=\${GALAXY_SLOTS:-1}
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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25 ./infile.${infile.ext}
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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26
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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27 > '$output'
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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28
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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29 ]]></command>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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30 <inputs>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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31 <param name="infile" type="data" format="xg,odgi" label="Graph files" />
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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32 <param argument="--path" type="text" value="" label="A reference path to deconstruct against"
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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33 help="comma-separated list accepted">
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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34 <sanitizer>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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35 <valid initial="string.printable">
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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36 <remove value="&apos;"/>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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37 </valid>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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38 </sanitizer>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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39 </param>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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40 <param argument="--path-prefix" type="text" value="" label="All paths beginning with this value used as reference"
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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41 help="comma-separated list accepted">
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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42 <sanitizer>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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43 <valid initial="string.printable">
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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44 <remove value="&apos;"/>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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45 </valid>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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46 </sanitizer>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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47 </param>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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48 <param argument="--alt-prefix" type="text" value="" label="Non-reference paths beginning with with this value get lumped together to same sample in VCF"
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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49 help="comma-separated list accepted">
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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50 <sanitizer>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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51 <valid initial="string.printable">
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52 <remove value="&apos;"/>
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53 </valid>
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54 </sanitizer>
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55 </param>
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56 <param argument="--snarls" type="data" format="xg,odgi" label="Snarls files" optional="true"
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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57 help="from `vg snarls` to avoid recomputing" />
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58
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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59 <param argument="--path-traversals" type="boolean" truevalue="--path-traversals" falsevalue="" checked="false"
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60 label="Only consider traversals that correspond to paths in the grpah" />
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61 </inputs>
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62 <outputs>
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63 <data name="output" format="vcf" />
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64 </outputs>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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65 <tests>
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66 <test>
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67 <param name="infile" value="hla.xg" />
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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68 <param name="path" value="gi|568815592:29791752-29792749" />
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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69 <param name="path_traversals" value="true" />
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70 <output name="output" file="hla_variants.vcf" />
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71 </test>
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72 </tests>
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73 <help><![CDATA[
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74 variation graph (vg) deconstruct module
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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75 -----------------------------------
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76
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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77 Creates VCF records for Snarls present in a graph (relative to a chosen reference path).
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78
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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79 ]]></help>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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80 <expand macro="citations">
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81 </expand>
a347dad1f305 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vg commit fc3deb5bce07a12b7f9bbd380118a7d2230a1003"
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82 </tool>