Mercurial > repos > iuc > bcftools_plugin_counts

annotate bcftools_plugin_counts.xml @ 14:28b35180900b draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
author iuc
date Thu, 14 Oct 2021 10:19:50 +0000
parents b781fa08aa3c
children 8d5d8355559b
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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@+galaxy1">
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3 <description>plugin counts number of samples, SNPs, INDELs, MNPs and total sites</description>
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4 <expand macro="bio_tools" />
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5 <macros>
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6 <token name="@EXECUTABLE@">counts</token>
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7 <token name="@PLUGIN_ID@">counts</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 <requirement type="package" version="3.7">python</requirement>
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12 </expand>
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13 <expand macro="version_command" />
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14 <command detect_errors="aggressive"><![CDATA[
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15 @PREPARE_ENV@
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16 @PREPARE_INPUT_FILE@
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17 #set $section = $sec_restrict
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18 @PREPARE_TARGETS_FILE@
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19 @PREPARE_REGIONS_FILE@
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20
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21 bcftools plugin @EXECUTABLE@
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23 ## VCF input section
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24 #set $section = $sec_restrict
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25 @INCLUDE@
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26 @EXCLUDE@
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27 @REGIONS@
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28 @TARGETS@
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29
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30 ## Primary Input/Outputs
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31 @INPUT_FILE@ | tee counts_file.txt
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32 && sed 's/^.* \([a-zA-Z]*\):[ ]*\([0-9]*\)$/\1 \2/' counts_file.txt | python $transform > '$output_file'
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33 ]]>
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34 </command>
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35 <configfiles>
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36 <configfile name="transform"><![CDATA[
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37 from __future__ import print_function
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38 import sys
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39 header = []
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40 value = []
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41 for line in sys.stdin:
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42 h,v = line.strip().split()
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43 header.append(h)
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44 value.append(v)
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45 print( '#%s' % '\t'.join(header) )
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46 print( '%s' % '\t'.join(value) )
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47 ]]>
0
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48 </configfile>
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49 </configfiles>
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50 <inputs>
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51 <expand macro="macro_input" />
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52 <section name="sec_restrict" expanded="false" title="Restrict to">
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53 <expand macro="macro_restrict" />
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54 <expand macro="macro_restrict" type="target" label_type="Target" />
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55 <expand macro="macro_include" />
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56 <expand macro="macro_exclude" />
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57 </section>
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58 </inputs>
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59 <outputs>
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60 <data name="output_file" format="tabular"/>
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61 </outputs>
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62 <tests>
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63 <test>
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64 <param name="input_file" ftype="vcf" value="view.vcf" />
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65 <output name="output_file">
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66 <assert_contents>
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67 <has_text text="SNPs"/>
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68 <has_text text="11"/>
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69 </assert_contents>
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70 </output>
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71 </test>
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72 </tests>
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73 <help><![CDATA[
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74 =====================================
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75 bcftools @EXECUTABLE@ plugin
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76 =====================================
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77
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78 Counts number of samples, SNPs, INDELs, MNPs and total number of sites.
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79
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80 @REGIONS_HELP@
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81 @TARGETS_HELP@
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82 @EXPRESSIONS_HELP@
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83
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84
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85
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86 ]]></help>
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87 <expand macro="citations" />
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88 </tool>