Mercurial > repos > iuc > crossmap_bed

annotate crossmap_bed.xml @ 10:50b7875a49d0 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
author iuc
date Mon, 02 Sep 2024 12:02:19 +0000
parents ee86b27291b5
children
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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"/>
10
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9 <!--
2
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10 1. CrossMap bed x.chain in.bed > out.bed
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11 stdout/out.bed: valid and invalid combined
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12
2
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13 2. CrossMap bed x.chain in.bed out.bed
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14 out.bed: valid only
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15 out.bed.unmap: invalid only
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16 -->
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17 <command><![CDATA[
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18 CrossMap bed
2
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19 '${chain_source.input_chain}'
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20 '${input}'
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21
2
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22 #if $merge_unmapped_entries:
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23 > '${output_combined}'
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24 #else:
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25 output
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26 --unmap-file output.unmap
2
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27 #end if
9
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28 --chromid $chromid
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29 ]]></command>
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30 <inputs>
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31 <param name="input" type="data" format="bed" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
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32 <expand macro="chain"/>
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33 <param name="chromid" type="select" label="Style of chromosome IDs">
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34 <option value="a" selected="true">As-is</option>
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35 <option value="l">Long style, e.g. chr1, chrX</option>
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36 <option value="s">Short style, e.g. 1, X</option>
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37 </param>
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38 <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/>
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39 </inputs>
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40 <outputs>
4
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41 <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}" from_work_dir="output">
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42 <filter>merge_unmapped_entries is False</filter>
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43 </data>
4
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44 <data name="output_failed" format="bed" label="${tool.name} (failed only) on ${on_string}" from_work_dir="output.unmap">
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45 <filter>merge_unmapped_entries is False</filter>
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46 </data>
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47 <data name="output_combined" format="bed" label="${tool.name} on ${on_string}">
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48 <filter>merge_unmapped_entries is True</filter>
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49 </data>
0
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50 </outputs>
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51 <tests>
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52 <test expect_num_outputs="2">
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53 <!-- this test only contains perfect entries that do get liftOvered (separate output) -->
2
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54 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
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55 <param name="index_source" value="history"/>
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56 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
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57 <param name="merge_unmapped_entries" value="false"/>
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58 <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/>
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59 <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/>
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60 </test>
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61 <test expect_num_outputs="1">
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62 <!-- this test only contains perfect entries that do get liftOvered (merged output) -->
2
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63 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
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64 <param name="index_source" value="history"/>
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65 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
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66 <param name="merge_unmapped_entries" value="true"/>
2
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67 <output name="output_combined" file="test_bed_01_output_a__all.bed"/>
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68 </test>
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69 <test expect_num_outputs="2">
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70 <!-- this test only contains imperfect entries that do get liftOvered (separate output) -->
2
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71 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
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72 <param name="index_source" value="history"/>
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73 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
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74 <param name="merge_unmapped_entries" value="false"/>
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75 <param name="chromid" value="s"/>
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76 <output name="output_valid" file="test_bed_02_output_a__only-matches.bed"/>
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77 <output name="output_failed" file="test_bed_02_output_a__only_fails.bed"/>
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78 </test>
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79 <test expect_num_outputs="1">
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80 <!-- this test only contains imperfect entries that do get liftOvered (separate output) -->
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81 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
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82 <param name="index_source" value="history"/>
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83 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
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84 <param name="merge_unmapped_entries" value="true"/>
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85 <param name="chromid" value="s"/>
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86 <output name="output_combined" file="test_bed_02_output_a__all.bed"/>
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87 </test>
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88 <test expect_num_outputs="2">
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89 <!-- clone of first test: tests cached reference chain file -->
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90 <param name="input" value="test_bed_01_input_a.bed" ftype="bed" dbkey="hg18"/>
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91 <param name="index_source" value="cached"/>
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92 <param name="merge_unmapped_entries" value="false"/>
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93 <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/>
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94 <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/>
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95 </test>
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96 </tests>
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97 <help><![CDATA[
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98 @HELP_GENERAL@
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99
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100 BED
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101 ---
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102
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103 BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns.
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104 BED format: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
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105
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106 A BED (Browser Extensible Data) file is a tab-delimited text file
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107 describing genome regions or gene annotations. It is the standard file
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108 format used by UCSC. It consists of one line per feature, each containing
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109 3-12 columns. CrossMap converts BED files with less than 12 columns to a
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110 different assembly by updating the chromosome and genome coordinates only;
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111 all other columns remain unchanged. Regions from old assembly mapping to
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112 multiple locations to the new assembly will be split. For 12-columns BED
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113 files, all columns will be updated accordingly except the 4th column (name
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114 of bed line), 5th column (score value) and 9th column (RGB value describing
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115 the display color). 12-column BED files usually define multiple blocks (eg.
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116 exon); if any of the exons fails to map to a new assembly, the whole BED
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117 line is skipped.
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118
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119 Notes:
0
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120
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121 1. For BED-like formats mentioned above, CrossMap only updates “chrom (1st
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122 column)”, “start (2nd column) ”, “end (3rd column) ” and “strand” (if
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123 any). All other columns will keep AS-IS.
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124 2. Lines starting with ‘#’, ‘browser’, ‘track’ will be skipped.
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125 3. Lines will less than 3 columns will be skipped.
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126 4. 2nd-column and 3-column must be integer, otherwise skipped.
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127 5. “+” strand is assumed if no strand information was found.
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128 6. For standard BED format (12 columns). If any of the defined exon blocks
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129 cannot be uniquely mapped to target assembly, the whole entry will be
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130 skipped.
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131 7. If input region cannot be consecutively mapped target assembly, it will be split.
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132 8. \*.unmap file contains regions that cannot be unambiguously converted.
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133 ]]></help>
0
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134 <citations>
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135 <citation type="doi">10.1093/bioinformatics/btt730</citation>
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136 </citations>
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137 </tool>