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annotate samtools_phase.xml @ 8:54bbc447e348 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_phase commit 8d2369dc1bdafc743920a155c508c20114ebe655
author iuc
date Mon, 17 Nov 2025 07:30:17 +0000
parents 2504000d5158
children
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54bbc447e348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_phase commit 8d2369dc1bdafc743920a155c508c20114ebe655
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1 <tool id="samtools_phase" name="Samtools phase" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>call and phase heterozygous SNPs</description>
3
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 samtools phase -b phase_wrapper
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11 #if str($option_set.option_sets) == 'advanced':
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12 ${option_set.ignore_chimeras}
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13 -k $option_set.block_length
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14 -q $option_set.min_het
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15 -Q $option_set.min_bq
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16 -D $option_set.read_depth
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17 ${option_set.drop_ambiguous}
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18 #else
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19 -k 13
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20 -q 37
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21 -Q 13
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22 -D 256
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23 #end if
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24 '$input_bam' > '$phase_sets'
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25 ]]></command>
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26 <inputs>
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27 <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/>
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28 <conditional name="option_set">
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29 <param name="option_sets" type="select" label="Phase parameters">
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30 <option value="default">Use defaults</option>
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31 <option value="advanced">Advanced options</option>
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32 </param>
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33 <when value="default" />
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34 <when value="advanced">
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35 <param name="block_length" argument="-k" type="integer" value="13" label="Maximum length for local phasing" />
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36 <param name="min_het" argument="-q" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" />
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37 <param name="min_bq" argument="-Q" type="integer" value="13" label="Minimum base quality to be used in het calling" />
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38 <param name="read_depth" argument="-D" type="integer" value="256" label="Read depth" />
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39 <param name="ignore_chimeras" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" />
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40 <param name="drop_ambiguous" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="False" label="Drop reads with ambiguous phase" />
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41 </when>
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42 </conditional>
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43 </inputs>
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44 <outputs>
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45 <data format="txt" name="phase_sets" />
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46 <data format="bam" from_work_dir="phase_wrapper.0.bam" name="phase0" label="${tool.name} on ${on_string}: Phase-0 reads" />
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47 <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${tool.name} on ${on_string}: Phase-1 reads" />
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48 <data format="bam" from_work_dir="phase_wrapper.chimera.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" />
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49 </outputs>
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50 <tests>
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51 <!-- 1) -->
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52 <test>
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53 <conditional name="option_set">
54bbc447e348 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools/samtools_phase commit 8d2369dc1bdafc743920a155c508c20114ebe655
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54 <param name="option_sets" value="default" />
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55 </conditional>
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56 <param name="input_bam" value="samtools_phase_in_1.bam" />
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57 <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt">
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58 <assert_contents>
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59 <has_text_matching expression="Descriptions:"/>
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60 </assert_contents>
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61 </output>
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62 <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" compare="sim_size"/>
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63 <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" compare="sim_size"/>
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64 <output name="chimera" file="empty_file_1.bam" ftype="bam" compare="sim_size"/>
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65 </test>
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66 <!-- 2) -->
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67 <test>
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68 <param name="input_bam" value="samtools_phase_in_2.bam" />
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69 <conditional name="option_set">
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70 <param name="option_sets" value="advanced" />
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71 </conditional>
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72 <param name="option_set|block_length" value="13" />
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73 <param name="option_set|min_het" value="37" />
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74 <param name="option_set|min_bq" value="13" />
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75 <param name="option_set|read_depth" value="256" />
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76 <param name="option_set|ignore_chimeras" value="false" />
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77 <param name="option_set|drop_ambiguous" value="true" />
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78 <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt">
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79 <assert_contents>
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80 <has_text_matching expression="Descriptions:"/>
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81 </assert_contents>
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82 </output>
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83 <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" compare="sim_size"/>
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84 <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" compare="sim_size"/>
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85 <output name="chimera" file="samtools_phase_out_2_chimera.bam" ftype="bam" compare="sim_size"/>
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86 </test>
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87 <!-- 3) -->
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88 <test>
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89 <param name="input_bam" value="samtools_phase_in_2.bam" />
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90 <conditional name="option_set">
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91 <param name="option_sets" value="advanced" />
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92 </conditional>
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93 <param name="option_set|block_length" value="13" />
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94 <param name="option_set|min_het" value="37" />
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95 <param name="option_set|min_bq" value="13" />
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96 <param name="option_set|read_depth" value="256" />
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97 <param name="option_set|ignore_chimeras" value="true" />
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98 <param name="option_set|drop_ambiguous" value="false" />
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99 <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt">
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100 <assert_contents>
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101 <has_text_matching expression="Descriptions:"/>
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102 </assert_contents>
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103 </output>
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104 <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" compare="sim_size"/>
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105 <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" compare="sim_size"/>
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106 <output name="chimera" file="empty_file_3.bam" ftype="bam" compare="sim_size"/>
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107 </test>
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108 </tests>
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109 <help><![CDATA[
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110 **What it does**
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111
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112 Call and phase heterozygous SNPs.
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113 ]]></help>
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114 <expand macro="citations"/>
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115 </tool>