Mercurial > repos > iuc > maf_stats
diff maf_stats.xml @ 0:5a92f4c476b5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ commit f7b04f8c6edca90b1e9bc867a1569996aec76d7a"
| author | iuc |
|---|---|
| date | Thu, 13 Aug 2020 09:30:47 -0400 |
| parents | |
| children | 0c84cce7b030 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/maf_stats.xml Thu Aug 13 09:30:47 2020 -0400 @@ -0,0 +1,130 @@ +<tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.1"> + <description>Alignment coverage information</description> + <command> + <![CDATA[ + #if $maf_source_type.maf_source == 'cached' + #set $tab = '\t' + echo '$maf_source_type.mafType.fields.name${tab}$maf_source_type.mafType.fields.value${tab}$maf_source_type.mafType.fields.indexed_for${tab}$maf_source_type.mafType.fields.exists_in_maf${tab}$maf_source_type.mafType.fields.path' >> ./maf_index.loc && + #end if + python '$__tool_directory__/maf_stats.py' $maf_source_type.maf_source + #if $maf_source_type.maf_source == 'user': + '$input2' + #else: + $maf_source_type.mafType.fields.value + #end if + '$input1' '$out_file1' $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary '.' + #if $maf_source_type.maf_source == 'user': + '$input2.metadata.maf_index' + #end if + ]]> + </command> + <inputs> + <param format="interval" name="input1" label="Interval File" type="data"> + <validator type="unspecified_build" /> + </param> + <conditional name="maf_source_type"> + <param name="maf_source" type="select" label="MAF Source"> + <option value="cached" selected="true">Locally Cached Alignments</option> + <option value="user">Alignments in Your History</option> + </param> + <when value="user"> + <param format="maf" name="input2" label="Choose alignments" type="data"> + <options> + <filter type="data_meta" ref="input1" key="dbkey" /> + </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"> + <options from_data_table="maf_indexes"> + <column name="name" index="0"/> + <column name="value" index="1"/> + <column name="indexed_for" index="2"/> + <column name="exists_in_maf" index="3" /> + <column name="path" index="4" /> + <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/> + <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/> + </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"> + <option value="false" selected="true">Coverage by Region</option> + <option value="true">Summarize Coverage</option> + </param> + </inputs> + <outputs> + <data format="interval" name="out_file1" metadata_source="input1"> + <change_format> + <when input="summary" value="true" format="tabular" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <param name="input1" value="maf_stats-in1.bed" dbkey="hg38" ftype="bed"/> + <param name="maf_source" value="cached"/> + <param name="mafType" value="TEST"/> + <output name="out_file1" file="maf_stats-out1.dat"/> + <param name="summary" value="false"/> + </test> + <test> + <param name="input1" value="maf_stats-in2.bed" dbkey="hg38" ftype="bed"/> + <param name="maf_source" value="cached"/> + <param name="mafType" value="TEST"/> + <output name="out_file1" file="maf_stats-out2.dat"/> + <param name="summary" value="true"/> + </test> + </tests> + <help> + **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. + + 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 M XXX YYY + + chrX 1000 1100 myInterval R XXX YYY + + + where XXX and YYY are: + + XXX = number of nucleotides + + YYY = number of gaps + + ---- + + 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 + ======== =========== ======== + + where **coverage** is the number of nucleotides divided by the total length of the provided intervals. + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btr398</citation> + </citations> +</tool>