Mercurial > repos > iuc > maf_stats
changeset 2:87c1c223c704 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit 1317f57940166a6326eea430443918f85b60bd95
| author | iuc |
|---|---|
| date | Wed, 25 Oct 2023 07:38:28 +0000 |
| parents | 0c84cce7b030 |
| children | |
| files | maf_stats.xml |
| diffstat | 1 files changed, 22 insertions(+), 33 deletions(-) [+] |
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--- a/maf_stats.xml Tue Nov 10 18:48:52 2020 +0000 +++ b/maf_stats.xml Wed Oct 25 07:38:28 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.1+galaxy0"> +<tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.2+galaxy0"> <description>Alignment coverage information</description> <command> <![CDATA[ @@ -34,11 +34,6 @@ </options> <validator type="dataset_ok_validator" /> </param> - <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment"> - <options> - <filter type="data_meta" ref="input2" key="species" /> - </options> - </param> </when> <when value="cached"> <param name="mafType" type="select" label="Choose alignments"> @@ -50,12 +45,6 @@ <column name="path" index="4" /> </options> </param> - <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment"> - <options from_data_table="maf_indexes"> - <column name="value" index="3"/> - <filter type="multiple_splitter" column="3" separator=","/> - </options> - </param> </when> </conditional> <param name="summary" type="select" label="Type of Output"> @@ -87,40 +76,40 @@ </test> </tests> <help> - **What it does** +**What it does** - This tool takes a MAF file and an interval file and relates coverage information by interval for each species. - If a column does not exist in the reference genome, it is not included in the output. +This tool takes an MAF file and an interval file and relates coverage information by interval for each species. +If a column does not exist in the reference genome, it is not included in the output. - Consider the interval: "chrX 1000 1100 myInterval" - Let's suppose we want to do stats on three way alignments for H, M, and R. The result look like this: +Consider the interval: "chrX 1000 1100 myInterval" +Let's suppose we want to do stats on three way alignments for H, M, and R. The result look like this: - chrX 1000 1100 myInterval H XXX YYY + chrX 1000 1100 myInterval H XXX YYY - chrX 1000 1100 myInterval M XXX YYY + chrX 1000 1100 myInterval M XXX YYY - chrX 1000 1100 myInterval R XXX YYY + chrX 1000 1100 myInterval R XXX YYY - where XXX and YYY are: +where XXX and YYY are: - XXX = number of nucleotides + XXX = number of nucleotides - YYY = number of gaps + YYY = number of gaps - ---- +---- - Alternatively, you can request only summary information for a set of intervals: +Alternatively, you can request only summary information for a set of intervals: - ======== =========== ======== - #species nucleotides coverage - ======== =========== ======== - hg18 30639 0.2372 - rheMac2 7524 0.0582 - panTro2 30390 0.2353 - ======== =========== ======== + ======== =========== ======== + #species nucleotides coverage + ======== =========== ======== + hg18 30639 0.2372 + rheMac2 7524 0.0582 + panTro2 30390 0.2353 + ======== =========== ======== - where **coverage** is the number of nucleotides divided by the total length of the provided intervals. +where **coverage** is the number of nucleotides divided by the total length of the intervals provided in the BED file. </help> <citations> <citation type="doi">10.1093/bioinformatics/btr398</citation>