annotate bcftools_plugin_impute_info.xml @ 13:dcf130f10ca5 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
author iuc
date Thu, 14 Oct 2021 10:07:43 +0000
parents 2c53c8974cb3
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@">
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3 <description>plugin Add imputation information metrics to the INFO field</description>
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4 <expand macro="bio_tools" />
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5 <macros>
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6 <token name="@EXECUTABLE@">impute-info</token>
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7 <token name="@PLUGIN_ID@">impute_info</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements" />
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11 <expand macro="version_command" />
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12 <command detect_errors="aggressive"><![CDATA[
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13 @PREPARE_ENV@
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14 @PREPARE_INPUT_FILE@
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15 #set $section = $sec_restrict
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16 @PREPARE_TARGETS_FILE@
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17 @PREPARE_REGIONS_FILE@
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19 bcftools plugin @EXECUTABLE@
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21 ## VCF input section
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22 #set $section = $sec_restrict
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23 @INCLUDE@
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24 @EXCLUDE@
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25 @REGIONS@
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26 @TARGETS@
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28 @OUTPUT_TYPE@
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29 @THREADS@
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31 ## Primary Input/Outputs
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32 @INPUT_FILE@
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33 > '$output_file'
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34 ]]>
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35 </command>
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36 <inputs>
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37 <expand macro="macro_input" />
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38 <section name="sec_restrict" expanded="false" title="Restrict to">
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39 <expand macro="macro_restrict" />
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40 <expand macro="macro_restrict" type="target" label_type="Target" />
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41 <expand macro="macro_include" />
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42 <expand macro="macro_exclude" />
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43 </section>
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44 <expand macro="macro_select_output_type" />
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45 </inputs>
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46 <outputs>
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47 <expand macro="macro_vcf_output" />
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="input_file" ftype="vcf" value="convert.vcf" />
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52 <param name="output_type" value="v" />
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53 <output name="output_file">
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54 <assert_contents>
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55 <has_text text="IMPUTE2" />
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56 <has_text text="INFO=1" />
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57 </assert_contents>
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58 </output>
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59 </test>
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60 </tests>
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61 <help><![CDATA[
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62 =====================================
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63 bcftools @EXECUTABLE@ plugin
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64 =====================================
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66 @REGIONS_HELP@
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67 @TARGETS_HELP@
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68 @EXPRESSIONS_HELP@
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70 ]]></help>
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71 <expand macro="citations" />
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72 </tool>