Mercurial > repos > iuc > pretext_map

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit c03782a5d213b2d272c0cbe9af2b7196fab2dc1c
author iuc
date Tue, 13 Feb 2024 21:59:50 +0000
parents 511e5e3cd55e
children
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1 <tool id="pretext_map" name="PretextMap" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
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2 <description>converts SAM or BAM files into genome contact maps</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">0.1.9</token>
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5 <token name="@VERSION_SUFFIX@">1</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">pretextmap</requirement>
6
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9 <requirement type="package" version="1.14">samtools</requirement>
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10 </requirements>
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11 <version_command>PretextMap --version</version_command>
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12 <command detect_errors="exit_code"><![CDATA[
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13 #if $input.is_of_type("bam"):
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14 samtools view -h '${input}' |
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15 #else
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16 cat '${input}' |
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17 #end if
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18 PretextMap
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19 #if $sorting.sortby == "length":
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20 --sortby length
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21 --sortorder $sorting.sortorder
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22 #elif $sorting.sortby == "name":
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23 --sortby name
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24 --sortorder $sorting.sortorder
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25 #end if
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26 #if str($map_qual):
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27 --mapq $map_qual
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28 #end if
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29 #if $filter.filter_type == "in":
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30 --filterInclude '$filter.filter_list'
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31 #elif $filter.filter_type == "out":
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32 --filterExclude '$filter.filter_list'
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33 #end if
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34 -o output.pretext
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35 ]]></command>
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36 <inputs>
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37 <param name="input" type="data" format="sam,bam" label="Input dataset in SAM or BAM format"/>
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38 <conditional name="sorting">
4
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39 <param argument="--sortby" type="select" label="Sort by" help="Sort the genome by length or name of the scaffolds">
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40 <option value="nosort">Don't sort</option>
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41 <option value="length" selected="true">Length</option>
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42 <option value="name">Name</option>
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43 </param>
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44 <when value="nosort"/>
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45 <when value="length">
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46 <param argument="--sortorder" type="select" label="Sort order: ">
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47 <option value="ascend">Ascending</option>
5
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48 <option value="descend">Descending</option>
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49 </param>
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50 </when>
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51 <when value="name">
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52 <param argument="--sortorder" type="select" label="Sort order: ">
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53 <option value="ascend">Ascending</option>
5
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54 <option value="descend">Descending</option>
0
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55 </param>
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56 </when>
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57 </conditional>
4
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58 <param name="map_qual" argument="--mapq" type="integer" label="Minimum mapping quality:" min="0" value="10" optional="true" help=" Filter mapped read by minimum MAPQ. Useful to remove spurious contacts from multimapping reads"/>
0
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59 <conditional name="filter">
4
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60 <param name="filter_type" type="select" label="How to filter: " help="Subset the output excluding a list of scaffolds">
0
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61 <option value="" selected="true">No filter</option>
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62 <option value="in">Filter to include only specified sequence names</option>
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63 <option value="out">Filter to exclude specified sequence names</option>
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64 </param>
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65 <when value=""/>
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66 <when value="in">
1
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67 <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1,seq_2">
0
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68 <sanitizer>
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69 <valid initial="string.ascii_letters,string.digits">
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70 <add value="_"/>
1
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71 <add value=","/>
0
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72 </valid>
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73 </sanitizer>
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74 </param>
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75 </when>
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76 <when value="out">
1
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77 <param name="filter_list" type="text" label="Filter list" help="Comma separated list of sequence names to use as a filter" value="seq_1,seq_2">
0
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78 <sanitizer>
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79 <valid initial="string.ascii_letters,string.digits">
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80 <add value="_"/>
1
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81 <add value=","/>
0
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82 </valid>
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83 </sanitizer>
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84 </param>
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85 </when>
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86 </conditional>
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87 </inputs>
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88 <outputs>
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89 <data format="pretext" name="pretext_map_out" from_work_dir="output.pretext" label="${tool.name} on ${on_string}"/>
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90 </outputs>
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91 <tests>
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92 <test>
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93 <param name="input" ftype="bam" value="test.bam"/>
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94 <conditional name="sorting">
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95 <param name="sortby" value="length"/>
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96 <param name="sortorder" value="ascend"/>
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97 </conditional>
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98 <conditional name="filter">
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99 <param name="filter_type" value="in"/>
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100 <param name="filter_list" value="ref"/>
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101 </conditional>
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102 <param name="map_qual" value="10"/>
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103 <output name="pretext_map_out" file="output_1.pretext"/>
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104 </test>
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105 <test>
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106 <param name="input" ftype="sam" value="test.sam"/>
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107 <conditional name="sorting">
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108 <param name="sortby" value="name"/>
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109 <param name="sortorder" value="descend"/>
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110 </conditional>
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111 <conditional name="filter">
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112 <param name="filter_type" value="out"/>
1
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113 <param name="filter_list" value="chrM,chr8,chr9"/>
0
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114 </conditional>
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115 <output name="pretext_map_out" file="output_2.pretext"/>
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116 </test>
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117 </tests>
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118 <help><![CDATA[
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119
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120 **What is does**
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121
4
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122 PretextMap (Paired REad TEXTure Mapper) converts SAM/BAM/CRAM or `pairs files <https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md>`_ into `genome contact maps <https://genome.ucsc.edu/goldenPath/help/hic.html>`_.
0
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123
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124 ]]></help>
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125 <citations>
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126 <citation type="bibtex">
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127 @misc{Harry_et_al,
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128 Author={Harry, E},
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129 title={Paired REad TEXTure Snapshot: Command line image generator for Pretext contact maps.},
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130 url = {https://github.com/wtsi-hpag/PretextSnapshot},}
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131 </citation>
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132 </citations>
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133 </tool>