Mercurial > repos > iuc > bcftools_plugin_color_chrs

annotate bcftools_plugin_color_chrs.xml @ 8:47ee1925fe9e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
author iuc
date Wed, 05 Jun 2019 12:59:21 -0400
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8
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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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 Color shared chromosomal segments, requires phased GTs</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">color-chrs</token>
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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6 <token name="@PLUGIN_ID@">color_chrs</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[
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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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 @PREPARE_REGIONS_FILE@
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17
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18 bcftools plugin @EXECUTABLE@
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19
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20 ## VCF input section
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21 #set $section = $sec_restrict
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22 @REGIONS@
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23 @TARGETS@
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24 @INCLUDE@
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25 @EXCLUDE@
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26
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27 @THREADS@
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28
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29 ## Primary Input/Outputs
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30 @INPUT_FILE@
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31
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32 ## Plugin options
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33 #if $sample_relation.sample_rel_sel == 'trio':
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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34 -- --trio '${sample_relation.mother},${sample_relation.father},${sample_relation.child}'
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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35 #else:
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36 -- --unrelated '${sample_relation.sample_a},${sample_relation.sample_b}'
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37 #end if
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38 -p output_tmp
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39 && color-chrs.pl output_tmp.dat -p output_tmp
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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40 && mv output_tmp.dat '$output_data'
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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41 && mv output_tmp.svg '$output_svg'
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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42 ]]>
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43 </command>
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44 <inputs>
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45 <expand macro="macro_input" />
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46 <conditional name="sample_relation">
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47 <param name="sample_rel_sel" type="select" label="Sample relationship">
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48 <option value="trio">trio - mother,father,child</option>
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49 <option value="unrelated">unrelated sample pair</option>
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50 </param>
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51 <when value="trio">
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52 <param name="mother" type="text" value="" label="name of mother"/>
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53 <param name="father" type="text" value="" label="name of father"/>
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54 <param name="child" type="text" value="" label="name of child"/>
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55 </when>
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56 <when value="unrelated">
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57 <param name="sample_a" type="text" value="" label="name of sample A"/>
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58 <param name="sample_b" type="text" value="" label="name of sample B"/>
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59 </when>
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60 </conditional>
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61 <section name="sec_restrict" expanded="false" title="Restrict analysis to">
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62 <expand macro="macro_include" />
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63 <expand macro="macro_exclude" />
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64 <expand macro="macro_restrict" />
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65 <expand macro="macro_restrict" type="target" label_type="Target" />
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66 </section>
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67 </inputs>
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68 <outputs>
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69 <data name="output_data" format="tabular" />
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70 <data name="output_svg" format="svg" />
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71 </outputs>
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72 <tests>
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73 <test expect_num_outputs="2">
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74 <param name="input_file" ftype="vcf" value="stats.a.vcf" />
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75 <conditional name="sample_relation">
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76 <param name="sample_rel_sel" value="trio" />
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77 <param name="mother" value="A" />
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78 <param name="father" value="C" />
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79 <param name="child" value="B" />
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80 </conditional>
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81 <output name="output_data" ftype="tabular" file="color_chrs.dat" />
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82 </test>
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83 <test expect_num_outputs="2">
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84 <param name="input_file" ftype="vcf" value="stats.a.vcf" />
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85 <conditional name="sample_relation">
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86 <param name="sample_rel_sel" value="unrelated" />
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87 <param name="sample_a" value="A" />
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88 <param name="sample_b" value="B" />
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89 </conditional>
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90 <output name="output_data" ftype="tabular" file="color_chrs_unrelated.dat" />
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91 </test>
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92 </tests>
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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93 <help><![CDATA[
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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94 =====================================
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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95 bcftools @EXECUTABLE@ plugin
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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96 =====================================
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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97
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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98 @REGIONS_HELP@
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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99 @TARGETS_HELP@
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100 @EXPRESSIONS_HELP@
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101
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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102 ]]>
47ee1925fe9e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
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103 </help>
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104 <expand macro="citations" />
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105 </tool>