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comparison 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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9:ee86b27291b5 10:50b7875a49d0
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 9 <!--
10 <!--
11 1. CrossMap bed x.chain in.bed > out.bed 10 1. CrossMap bed x.chain in.bed > out.bed
12 stdout/out.bed: valid and invalid combined 11 stdout/out.bed: valid and invalid combined
13 12
14 2. CrossMap bed x.chain in.bed out.bed 13 2. CrossMap bed x.chain in.bed out.bed
15 out.bed: valid only 14 out.bed: valid only
16 out.bed.unmap: invalid only 15 out.bed.unmap: invalid only
17 --> 16 -->
18 <command><![CDATA[ 17 <command><![CDATA[
19 CrossMap.py bed 18 CrossMap bed
20 '${chain_source.input_chain}' 19 '${chain_source.input_chain}'
21 '${input}' 20 '${input}'
22 21
23 #if $merge_unmapped_entries: 22 #if $merge_unmapped_entries:
24 > '${output_combined}' 23 > '${output_combined}'
26 output 25 output
27 --unmap-file output.unmap 26 --unmap-file output.unmap
28 #end if 27 #end if
29 --chromid $chromid 28 --chromid $chromid
30 ]]></command> 29 ]]></command>
31
32
33 <inputs> 30 <inputs>
34 <param name="input" type="data" format="bed" label="BED file" 31 <param name="input" type="data" format="bed" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/>
35 help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/> 32 <expand macro="chain"/>
36
37 <expand macro="chain" />
38 <param name="chromid" type="select" label="Style of chromosome IDs"> 33 <param name="chromid" type="select" label="Style of chromosome IDs">
39 <option value="a" selected="true">As-is</option> 34 <option value="a" selected="true">As-is</option>
40 <option value="l">Long style, e.g. chr1, chrX</option> 35 <option value="l">Long style, e.g. chr1, chrX</option>
41 <option value="s">Short style, e.g. 1, X</option> 36 <option value="s">Short style, e.g. 1, X</option>
42 </param> 37 </param>
43 <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/> 38 <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/>
44 </inputs> 39 </inputs>
45
46 <outputs> 40 <outputs>
47 <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}" from_work_dir="output"> 41 <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}" from_work_dir="output">
48 <filter>merge_unmapped_entries is False</filter> 42 <filter>merge_unmapped_entries is False</filter>
49 </data> 43 </data>
50 <data name="output_failed" format="bed" label="${tool.name} (failed only) on ${on_string}" from_work_dir="output.unmap"> 44 <data name="output_failed" format="bed" label="${tool.name} (failed only) on ${on_string}" from_work_dir="output.unmap">
51 <filter>merge_unmapped_entries is False</filter> 45 <filter>merge_unmapped_entries is False</filter>
52 </data> 46 </data>
53
54 <data name="output_combined" format="bed" label="${tool.name} on ${on_string}"> 47 <data name="output_combined" format="bed" label="${tool.name} on ${on_string}">
55 <filter>merge_unmapped_entries is True</filter> 48 <filter>merge_unmapped_entries is True</filter>
56 </data> 49 </data>
57 </outputs> 50 </outputs>
58
59 <tests> 51 <tests>
60 <test><!-- this test only contains perfect entries that do get liftOvered (separate output) --> 52 <test expect_num_outputs="2">
53 <!-- this test only contains perfect entries that do get liftOvered (separate output) -->
61 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/> 54 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
62 <param name="index_source" value="history"/> 55 <param name="index_source" value="history"/>
63 <param name="input_chain" value="aToB.over.chain" ftype="csv"/> 56 <param name="input_chain" value="aToB.over.chain" ftype="csv"/>
64 <param name="merge_unmapped_entries" value="false" /> 57 <param name="merge_unmapped_entries" value="false"/>
65
66 <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/> 58 <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/>
67 <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/> 59 <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/>
68 </test> 60 </test>
69 <test><!-- this test only contains perfect entries that do get liftOvered (merged output) --> 61 <test expect_num_outputs="1">
62 <!-- this test only contains perfect entries that do get liftOvered (merged output) -->
70 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/> 63 <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/>
71 <param name="index_source" value="history"/> 64 <param name="index_source" value="history"/>
72 <param name="input_chain" value="aToB.over.chain" ftype="txt"/> 65 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
73 <param name="merge_unmapped_entries" value="true" /> 66 <param name="merge_unmapped_entries" value="true"/>
74
75 <output name="output_combined" file="test_bed_01_output_a__all.bed"/> 67 <output name="output_combined" file="test_bed_01_output_a__all.bed"/>
76 </test> 68 </test>
77 69 <test expect_num_outputs="2">
78 <test><!-- this test only contains imperfect entries that do get liftOvered (separate output) --> 70 <!-- this test only contains imperfect entries that do get liftOvered (separate output) -->
79 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/> 71 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
80 <param name="index_source" value="history"/> 72 <param name="index_source" value="history"/>
81 <param name="input_chain" value="aToB.over.chain" ftype="txt"/> 73 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
82 <param name="merge_unmapped_entries" value="false" /> 74 <param name="merge_unmapped_entries" value="false"/>
83 <param name="chromid" value="s" /> 75 <param name="chromid" value="s"/>
84
85 <output name="output_valid" file="test_bed_02_output_a__only-matches.bed"/> 76 <output name="output_valid" file="test_bed_02_output_a__only-matches.bed"/>
86 <output name="output_failed" file="test_bed_02_output_a__only_fails.bed"/> 77 <output name="output_failed" file="test_bed_02_output_a__only_fails.bed"/>
87 </test> 78 </test>
88 <test><!-- this test only contains imperfect entries that do get liftOvered (separate output) --> 79 <test expect_num_outputs="1">
80 <!-- this test only contains imperfect entries that do get liftOvered (separate output) -->
89 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/> 81 <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/>
90 <param name="index_source" value="history"/> 82 <param name="index_source" value="history"/>
91 <param name="input_chain" value="aToB.over.chain" ftype="txt"/> 83 <param name="input_chain" value="aToB.over.chain" ftype="txt"/>
92 <param name="merge_unmapped_entries" value="true" /> 84 <param name="merge_unmapped_entries" value="true"/>
93 <param name="chromid" value="s" /> 85 <param name="chromid" value="s"/>
94
95 <output name="output_combined" file="test_bed_02_output_a__all.bed"/> 86 <output name="output_combined" file="test_bed_02_output_a__all.bed"/>
96 </test> 87 </test>
97 88 <test expect_num_outputs="2">
98 <test><!-- clone of first test: tests cached reference chain file --> 89 <!-- clone of first test: tests cached reference chain file -->
99 <param name="input" value="test_bed_01_input_a.bed" ftype="bed" dbkey="hg18"/> 90 <param name="input" value="test_bed_01_input_a.bed" ftype="bed" dbkey="hg18"/>
100 <param name="index_source" value="cached"/> 91 <param name="index_source" value="cached"/>
101 <param name="merge_unmapped_entries" value="false" /> 92 <param name="merge_unmapped_entries" value="false"/>
102
103 <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/> 93 <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/>
104 <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/> 94 <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/>
105 </test> 95 </test>
106 </tests> 96 </tests>
107 <help><![CDATA[ 97 <help><![CDATA[
139 cannot be uniquely mapped to target assembly, the whole entry will be 129 cannot be uniquely mapped to target assembly, the whole entry will be
140 skipped. 130 skipped.
141 7. If input region cannot be consecutively mapped target assembly, it will be split. 131 7. If input region cannot be consecutively mapped target assembly, it will be split.
142 8. \*.unmap file contains regions that cannot be unambiguously converted. 132 8. \*.unmap file contains regions that cannot be unambiguously converted.
143 ]]></help> 133 ]]></help>
144
145 <citations> 134 <citations>
146 <citation type="doi">10.1093/bioinformatics/btt730</citation> 135 <citation type="doi">10.1093/bioinformatics/btt730</citation>
147 </citations> 136 </citations>
148 </tool> 137 </tool>