Mercurial > repos > iuc > crossmap_bed

annotate crossmap_bed.xml @ 9:ee86b27291b5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"
author iuc
date Thu, 20 Jan 2022 04:31:56 +0000
parents f4a70882a71b
children 50b7875a49d0
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f4a70882a71b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"
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1 <tool id="crossmap_bed" name="CrossMap BED" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>Convert genome coordinates or annotation files between genome assemblies</description>
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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
2
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10 <!--
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11 1. CrossMap bed x.chain in.bed > out.bed
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12 stdout/out.bed: valid and invalid combined
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13
2
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14 2. CrossMap bed x.chain in.bed out.bed
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15 out.bed: valid only
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16 out.bed.unmap: invalid only
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17 -->
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18 <command><![CDATA[
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19 CrossMap.py bed
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20 '${chain_source.input_chain}'
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21 '${input}'
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22
2
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23 #if $merge_unmapped_entries:
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24 > '${output_combined}'
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25 #else:
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26 output
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27 --unmap-file output.unmap
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28 #end if
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29 --chromid $chromid
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30 ]]></command>
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33 <inputs>
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34 <param name="input" type="data" format="bed" label="BED file"
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35 help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
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37 <expand macro="chain" />
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38 <param name="chromid" type="select" label="Style of chromosome IDs">
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39 <option value="a" selected="true">As-is</option>
ee86b27291b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"
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40 <option value="l">Long style, e.g. chr1, chrX</option>
ee86b27291b5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"
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41 <option value="s">Short style, e.g. 1, X</option>
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42 </param>
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43 <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/>
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44 </inputs>
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46 <outputs>
4
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47 <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}" from_work_dir="output">
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48 <filter>merge_unmapped_entries is False</filter>
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49 </data>
4
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50 <data name="output_failed" format="bed" label="${tool.name} (failed only) on ${on_string}" from_work_dir="output.unmap">
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51 <filter>merge_unmapped_entries is False</filter>
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52 </data>
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53
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54 <data name="output_combined" format="bed" label="${tool.name} on ${on_string}">
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55 <filter>merge_unmapped_entries is True</filter>
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56 </data>
0
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57 </outputs>
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59 <tests>
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60 <test><!-- this test only contains perfect entries that do get liftOvered (separate output) -->
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61 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
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62 <param name="index_source" value="history"/>
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63 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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64 <param name="merge_unmapped_entries" value="false" />
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65
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66 <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/>
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67 <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/>
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68 </test>
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69 <test><!-- this test only contains perfect entries that do get liftOvered (merged output) -->
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70 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
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71 <param name="index_source" value="history"/>
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72 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
2
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73 <param name="merge_unmapped_entries" value="true" />
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75 <output name="output_combined" file="test_bed_01_output_a__all.bed"/>
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76 </test>
0
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77
2
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78 <test><!-- this test only contains imperfect entries that do get liftOvered (separate output) -->
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79 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
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80 <param name="index_source" value="history"/>
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81 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
2
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82 <param name="merge_unmapped_entries" value="false" />
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83 <param name="chromid" value="s" />
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84
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85 <output name="output_valid" file="test_bed_02_output_a__only-matches.bed"/>
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86 <output name="output_failed" file="test_bed_02_output_a__only_fails.bed"/>
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87 </test>
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88 <test><!-- this test only contains imperfect entries that do get liftOvered (separate output) -->
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89 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
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90 <param name="index_source" value="history"/>
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91 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
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92 <param name="merge_unmapped_entries" value="true" />
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93 <param name="chromid" value="s" />
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94
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95 <output name="output_combined" file="test_bed_02_output_a__all.bed"/>
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96 </test>
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97
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98 <test><!-- clone of first test: tests cached reference chain file -->
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99 <param name="input" value="test_bed_01_input_a.bed" ftype="bed" dbkey="hg18"/>
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100 <param name="index_source" value="cached"/>
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101 <param name="merge_unmapped_entries" value="false" />
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102
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103 <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/>
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104 <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/>
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105 </test>
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106 </tests>
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107 <help><![CDATA[
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108 @HELP_GENERAL@
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109
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110 BED
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111 ---
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112
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113 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
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114 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
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115
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116 A BED (Browser Extensible Data) file is a tab-delimited text file
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117 describing genome regions or gene annotations. It is the standard file
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118 format used by UCSC. It consists of one line per feature, each containing
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119 3-12 columns. CrossMap converts BED files with less than 12 columns to a
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120 different assembly by updating the chromosome and genome coordinates only;
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121 all other columns remain unchanged. Regions from old assembly mapping to
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122 multiple locations to the new assembly will be split. For 12-columns BED
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123 files, all columns will be updated accordingly except the 4th column (name
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124 of bed line), 5th column (score value) and 9th column (RGB value describing
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125 the display color). 12-column BED files usually define multiple blocks (eg.
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126 exon); if any of the exons fails to map to a new assembly, the whole BED
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127 line is skipped.
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128
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129 Notes:
0
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130
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131 1. For BED-like formats mentioned above, CrossMap only updates “chrom (1st
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132 column)”, “start (2nd column) ”, “end (3rd column) ” and “strand” (if
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133 any). All other columns will keep AS-IS.
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134 2. Lines starting with ‘#’, ‘browser’, ‘track’ will be skipped.
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135 3. Lines will less than 3 columns will be skipped.
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136 4. 2nd-column and 3-column must be integer, otherwise skipped.
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137 5. “+” strand is assumed if no strand information was found.
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138 6. For standard BED format (12 columns). If any of the defined exon blocks
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139 cannot be uniquely mapped to target assembly, the whole entry will be
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140 skipped.
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141 7. If input region cannot be consecutively mapped target assembly, it will be split.
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142 8. \*.unmap file contains regions that cannot be unambiguously converted.
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143 ]]></help>
0
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144
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145 <citations>
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146 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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147 </citations>
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148 </tool>