Mercurial > repos > iuc > bcftools_plugin_tag2tag

annotate bcftools_plugin_tag2tag.xml @ 0:702c96a52e74 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 07:07:45 -0400
parents
children 09533c5972fb
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0
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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1 <?xml version='1.0' encoding='utf-8'?>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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3 <description>plugin Convert between similar tags, such as GL and GP</description>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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4 <macros>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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5 <token name="@EXECUTABLE@">tag2tag</token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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6 <token name="@PLUGIN_ID@">tag2tag</token>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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7 <import>macros.xml</import>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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8 </macros>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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9 <expand macro="requirements" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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10 <expand macro="version_command" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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11 <command detect_errors="aggressive"><![CDATA[
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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12 @PREPARE_ENV@
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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13 @PREPARE_INPUT_FILE@
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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14 #set $section = $sec_restrict
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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15 @PREPARE_TARGETS_FILE@
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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16
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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17 bcftools plugin @EXECUTABLE@
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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18
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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19 ## VCF input section
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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20 #set $section = $sec_restrict
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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21 @INCLUDE@
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22 @EXCLUDE@
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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23 @REGIONS@
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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24 @TARGETS@
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25
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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26 @OUTPUT_TYPE@
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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27 @THREADS@
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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28
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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29 ## Primary Input/Outputs
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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30 @INPUT_FILE@
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31
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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32 ## Plugin section
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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33 #set $section = $sec_plugin
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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34 --
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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35 ${section.conversion}
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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36 ${section.replace}
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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37 > "$output_file"
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38 ]]>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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39 </command>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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40 <inputs>
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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41 <expand macro="macro_input" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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42 <section name="sec_restrict" expanded="false" title="Restrict to">
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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43 <expand macro="macro_regions" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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44 <expand macro="macro_targets" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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45 <expand macro="macro_include" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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46 <expand macro="macro_exclude" />
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47 </section>
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48 <section name="sec_plugin" expanded="true" title="Plugin Options">
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49 <param name="conversion" type="select" label="Tag conversion">
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50 <option value="--gp-to-gl" selected="true">convert FORMAT/GP to FORMAT/GL</option>
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51 <option value="--gl-to-pl">convert FORMAT/GL to FORMAT/PL</option>
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52 </param>
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53 <param name="replace" type="boolean" truevalue="--replace" falsevalue="" checked="true" label="drop the source tag" help="(\-\-replace)" />
702c96a52e74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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54 </section>
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55 <expand macro="macro_select_output_type" />
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56 </inputs>
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57 <outputs>
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58 <expand macro="macro_vcf_output" />
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59 </outputs>
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60 <tests>
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61 <test>
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62 <param name="input_file" ftype="vcf" value="view.GL.vcf" />
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63 <param name="replace" value="True" />
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64 <param name="conversion" value="--gp-to-gl" />
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65 <param name="output_type" value="v" />
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66 <output name="output_file">
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67 <assert_contents>
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68 </assert_contents>
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69 </output>
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70 </test>
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71 </tests>
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72 <help><![CDATA[
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73 =====================================
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74 bcftools @EXECUTABLE@ plugin
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75 =====================================
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76
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77 @REGIONS_HELP@
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78 @TARGETS_HELP@
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79 @EXPRESSIONS_HELP@
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80
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81 ]]></help>
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82 <expand macro="citations" />
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83 </tool>