Mercurial > repos > iuc > bcftools_plugin_counts

annotate bcftools_plugin_counts.xml @ 11:d8dddb51e831 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f3fe2272c80fdb749db49be689681e4d1391bee"
author iuc
date Wed, 25 Dec 2019 12:30:22 -0500
parents ed2ebaaded62
children b781fa08aa3c
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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 counts number of samples, SNPs, INDELs, MNPs and total sites</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">counts</token>
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6 <token name="@PLUGIN_ID@">counts</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 <requirement type="package" version="3.7">pyton</requirement>
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11 </expand>
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12 <expand macro="version_command" />
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13 <command detect_errors="aggressive"><![CDATA[
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14 @PREPARE_ENV@
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15 @PREPARE_INPUT_FILE@
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16 #set $section = $sec_restrict
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17 @PREPARE_TARGETS_FILE@
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18 @PREPARE_REGIONS_FILE@
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19
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20 bcftools plugin @EXECUTABLE@
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21
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22 ## VCF input section
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23 #set $section = $sec_restrict
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24 @INCLUDE@
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25 @EXCLUDE@
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26 @REGIONS@
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27 @TARGETS@
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28
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29 ## Primary Input/Outputs
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30 @INPUT_FILE@ | tee counts_file.txt
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31 && sed 's/^.* \([a-zA-Z]*\):[ ]*\([0-9]*\)$/\1 \2/' counts_file.txt | python $transform > '$output_file'
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32 ]]>
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33 </command>
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34 <configfiles>
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35 <configfile name="transform"><![CDATA[
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36 from __future__ import print_function
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37 import sys
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38 header = []
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39 value = []
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40 for line in sys.stdin:
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41 h,v = line.strip().split()
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42 header.append(h)
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43 value.append(v)
3
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44 print( '#%s' % '\t'.join(header) )
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45 print( '%s' % '\t'.join(value) )
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46 ]]>
0
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47 </configfile>
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48 </configfiles>
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49 <inputs>
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50 <expand macro="macro_input" />
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51 <section name="sec_restrict" expanded="false" title="Restrict to">
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52 <expand macro="macro_restrict" />
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53 <expand macro="macro_restrict" type="target" label_type="Target" />
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54 <expand macro="macro_include" />
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55 <expand macro="macro_exclude" />
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56 </section>
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57 </inputs>
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58 <outputs>
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59 <data name="output_file" format="tabular"/>
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="input_file" ftype="vcf" value="view.vcf" />
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64 <output name="output_file">
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65 <assert_contents>
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66 <has_text text="SNPs"/>
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67 <has_text text="11"/>
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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 Counts number of samples, SNPs, INDELs, MNPs and total number of sites.
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78
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79 @REGIONS_HELP@
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80 @TARGETS_HELP@
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81 @EXPRESSIONS_HELP@
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82
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84
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85 ]]></help>
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86 <expand macro="citations" />
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87 </tool>