| Previous changeset 9:ee86b27291b5 (2022-01-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568 |
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modified:
crossmap_bed.xml macros.xml |
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| diff -r ee86b27291b5 -r 50b7875a49d0 crossmap_bed.xml --- a/crossmap_bed.xml Thu Jan 20 04:31:56 2022 +0000 +++ b/crossmap_bed.xml Mon Sep 02 12:02:19 2024 +0000 |
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| @@ -6,8 +6,7 @@ <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> - -<!-- + <!-- 1. CrossMap bed x.chain in.bed > out.bed stdout/out.bed: valid and invalid combined @@ -16,7 +15,7 @@ out.bed.unmap: invalid only --> <command><![CDATA[ -CrossMap.py bed +CrossMap bed '${chain_source.input_chain}' '${input}' @@ -28,13 +27,9 @@ #end if --chromid $chromid ]]></command> - - <inputs> - <param name="input" type="data" format="bed" label="BED file" - help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/> - - <expand macro="chain" /> + <param name="input" type="data" format="bed" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns"/> + <expand macro="chain"/> <param name="chromid" type="select" label="Style of chromosome IDs"> <option value="a" selected="true">As-is</option> <option value="l">Long style, e.g. chr1, chrX</option> @@ -42,7 +37,6 @@ </param> <param name="merge_unmapped_entries" type="boolean" checked="false" truevalue="true" falsevalue="false" label="Merge failed and converted entries into single file"/> </inputs> - <outputs> <data name="output_valid" format="bed" label="${tool.name} (valid only) on ${on_string}" from_work_dir="output"> <filter>merge_unmapped_entries is False</filter> @@ -50,56 +44,52 @@ <data name="output_failed" format="bed" label="${tool.name} (failed only) on ${on_string}" from_work_dir="output.unmap"> <filter>merge_unmapped_entries is False</filter> </data> - <data name="output_combined" format="bed" label="${tool.name} on ${on_string}"> <filter>merge_unmapped_entries is True</filter> </data> </outputs> - <tests> - <test><!-- this test only contains perfect entries that do get liftOvered (separate output) --> + <test expect_num_outputs="2"> + <!-- this test only contains perfect entries that do get liftOvered (separate output) --> <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/> <param name="index_source" value="history"/> <param name="input_chain" value="aToB.over.chain" ftype="csv"/> - <param name="merge_unmapped_entries" value="false" /> - + <param name="merge_unmapped_entries" value="false"/> <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/> <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/> </test> - <test><!-- this test only contains perfect entries that do get liftOvered (merged output) --> + <test expect_num_outputs="1"> + <!-- this test only contains perfect entries that do get liftOvered (merged output) --> <param name="input" value="test_bed_01_input_a.bed" ftype="bed"/> <param name="index_source" value="history"/> <param name="input_chain" value="aToB.over.chain" ftype="txt"/> - <param name="merge_unmapped_entries" value="true" /> - + <param name="merge_unmapped_entries" value="true"/> <output name="output_combined" file="test_bed_01_output_a__all.bed"/> </test> - - <test><!-- this test only contains imperfect entries that do get liftOvered (separate output) --> + <test expect_num_outputs="2"> + <!-- this test only contains imperfect entries that do get liftOvered (separate output) --> <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/> <param name="index_source" value="history"/> <param name="input_chain" value="aToB.over.chain" ftype="txt"/> - <param name="merge_unmapped_entries" value="false" /> - <param name="chromid" value="s" /> - + <param name="merge_unmapped_entries" value="false"/> + <param name="chromid" value="s"/> <output name="output_valid" file="test_bed_02_output_a__only-matches.bed"/> <output name="output_failed" file="test_bed_02_output_a__only_fails.bed"/> </test> - <test><!-- this test only contains imperfect entries that do get liftOvered (separate output) --> + <test expect_num_outputs="1"> + <!-- this test only contains imperfect entries that do get liftOvered (separate output) --> <param name="input" value="test_bed_02_input_a.bed" ftype="bed"/> <param name="index_source" value="history"/> <param name="input_chain" value="aToB.over.chain" ftype="txt"/> - <param name="merge_unmapped_entries" value="true" /> - <param name="chromid" value="s" /> - + <param name="merge_unmapped_entries" value="true"/> + <param name="chromid" value="s"/> <output name="output_combined" file="test_bed_02_output_a__all.bed"/> </test> - - <test><!-- clone of first test: tests cached reference chain file --> + <test expect_num_outputs="2"> + <!-- clone of first test: tests cached reference chain file --> <param name="input" value="test_bed_01_input_a.bed" ftype="bed" dbkey="hg18"/> <param name="index_source" value="cached"/> - <param name="merge_unmapped_entries" value="false" /> - + <param name="merge_unmapped_entries" value="false"/> <output name="output_valid" file="test_bed_01_output_a__only-matches.bed"/> <output name="output_failed" file="test_bed_01_output_a__only_fails.bed"/> </test> @@ -141,7 +131,6 @@ 7. If input region cannot be consecutively mapped target assembly, it will be split. 8. \*.unmap file contains regions that cannot be unambiguously converted. ]]></help> - <citations> <citation type="doi">10.1093/bioinformatics/btt730</citation> </citations> |
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| diff -r ee86b27291b5 -r 50b7875a49d0 macros.xml --- a/macros.xml Thu Jan 20 04:31:56 2022 +0000 +++ b/macros.xml Mon Sep 02 12:02:19 2024 +0000 |
| [ |
| @@ -1,4 +1,3 @@ -<?xml version="1.0"?> <macros> <xml name="requirements"> <requirements> @@ -6,7 +5,7 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">0.6.1</token> + <token name="@TOOL_VERSION@">0.7.0</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="stdio"> <stdio> @@ -17,7 +16,7 @@ </xml> <xml name="version_command"> <version_command><![CDATA[ -CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*' +CrossMap 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*' ]]></version_command> </xml> <xml name="chain"> |