Mercurial > repos > jjohnson > bcftools_plugin_fill_an_ac

annotate bcftools_plugin_fill_an_ac.xml @ 0:e1277c44ebd5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sat, 25 Jun 2016 20:49:40 -0400
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e1277c44ebd5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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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="@VERSION@.0">
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3 <description>plugin Fill INFO fields AN and AC</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">fill-AN-AC</token>
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6 <token name="@PLUGIN_ID@">fill_an_ac</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements" />
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10 <expand macro="version_command" />
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11 <command detect_errors="aggressive"><![CDATA[
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12 @PREPARE_ENV@
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13 @PREPARE_INPUT_FILE@
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14 #set $section = $sec_restrict
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15 @PREPARE_TARGETS_FILE@
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16
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17 bcftools plugin @EXECUTABLE@
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18 ## VCF input section
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19 #set $section = $sec_restrict
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20 @INCLUDE@
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21 @EXCLUDE@
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22 @REGIONS@
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23 @TARGETS@
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24
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25 @OUTPUT_TYPE@
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26 @THREADS@
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27
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28 ## Primary Input/Outputs
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29 @INPUT_FILE@
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30 > "$output_file"
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31 ]]>
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32 </command>
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33 <inputs>
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34 <expand macro="macro_input" />
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35 <section name="sec_restrict" expanded="false" title="Restrict to">
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36 <expand macro="macro_regions" />
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37 <expand macro="macro_targets" />
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38 <expand macro="macro_include" />
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39 <expand macro="macro_exclude" />
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40 </section>
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41 <expand macro="macro_select_output_type" />
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42 </inputs>
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43 <outputs>
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44 <expand macro="macro_vcf_output" />
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="input_file" ftype="vcf" value="plugin1.vcf" />
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49 <param name="output_type" value="v" />
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50 <output name="output_file">
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51 <assert_contents>
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52 <has_text text="AN=0;AC=0" />
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53 </assert_contents>
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54 </output>
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58 =====================================
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59 bcftools @EXECUTABLE@ plugin
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60 =====================================
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61
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62 @REGIONS_HELP@
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63 @TARGETS_HELP@
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64 @EXPRESSIONS_HELP@
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65
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66 ]]></help>
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67 <expand macro="citations" />
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68 </tool>