mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
James Taylor
bb769367ed
configured at the application level. Specific tabular data files are specified in a application config file and bound to names, the tools then refer to these names. Thus users can configure where location files are located without modifying tool configs. Also: - Simpler column name configuration - Columns can be referred to by name in addition to index in all dynamic option filters - A data table can merge multiple files - Design can support other types of data files
117 lines
6.7 KiB
XML
117 lines
6.7 KiB
XML
<tool id="Interval2Maf1" name="Extract MAF blocks" version="1.0.1">
|
|
<description>given a set of genomic intervals</description>
|
|
<command interpreter="python">
|
|
#if $maf_source_type.maf_source == "user" #interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafFile=$maf_source_type.mafFile --mafIndex=$maf_source_type.mafFile.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species
|
|
#else #interval2maf.py --dbkey=${input1.dbkey} --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafType=$maf_source_type.mafType --interval_file=$input1 --output_file=$out_file1 --mafIndexFile=${GALAXY_DATA_INDEX_DIR}/maf_index.loc --species=$maf_source_type.species
|
|
#end if# --split_blocks_by_species=$split_blocks_by_species_selector.split_blocks_by_species
|
|
#if $split_blocks_by_species_selector.split_blocks_by_species == "split_blocks_by_species"#
|
|
--remove_all_gap_columns=$split_blocks_by_species_selector.remove_all_gap_columns
|
|
#end if
|
|
</command>
|
|
<inputs>
|
|
<param format="interval" name="input1" type="data" label="Choose intervals">
|
|
<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="mafFile" 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="mafFile" key="species" />
|
|
</options>
|
|
</param>
|
|
</when>
|
|
<when value="cached">
|
|
<param name="mafType" type="select" label="Choose alignments">
|
|
<options from_data_table="indexed_maf_files">
|
|
<!--
|
|
<column name="name" index="0"/>
|
|
<column name="value" index="1"/>
|
|
<column name="dbkey" index="2"/>
|
|
<column name="species" index="3"/>
|
|
-->
|
|
<filter type="data_meta" ref="input1" key="dbkey" column="dbkey" 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="indexed_maf_files">
|
|
<column name="uid" index="1"/>
|
|
<column name="value" index="3"/>
|
|
<column name="name" index="3"/>
|
|
<filter type="param_value" ref="mafType" column="uid"/>
|
|
<filter type="multiple_splitter" column="name" separator=","/>
|
|
</options>
|
|
</param>
|
|
</when>
|
|
</conditional>
|
|
<conditional name="split_blocks_by_species_selector">
|
|
<param name="split_blocks_by_species" type="select" label="Split blocks by species" help="See the Split MAF blocks by Species tool for more information.">
|
|
<option value="split_blocks_by_species">Split by species</option>
|
|
<option value="dont_split_blocks_by_species" selected="true">Do not split</option>
|
|
</param>
|
|
<when value="dont_split_blocks_by_species">
|
|
<!-- do nothing here -->
|
|
</when>
|
|
<when value="split_blocks_by_species">
|
|
<param name="remove_all_gap_columns" type="select" label="Collapse empty alignment columns">
|
|
<option value="remove_all_gap_columns" selected="true">Collapse empty columns</option>
|
|
<option value="do_not_remove_all_gap_columns">Do not collapse</option>
|
|
</param>
|
|
</when>
|
|
</conditional>
|
|
</inputs>
|
|
<outputs>
|
|
<data format="maf" name="out_file1"/>
|
|
</outputs>
|
|
<tests>
|
|
<test>
|
|
<param name="input1" value="1.bed"/>
|
|
<param name="maf_source" value="cached"/>
|
|
<param name="mafType" value="ENCODE_TBA_hg17"/>
|
|
<param name="species" value="hg17,panTro1,baboon,marmoset,galago,rn3,mm6,rabbit,cow,canFam1,rfbat,shrew,armadillo,tenrec,monDom1,tetNig1,fr1,rheMac1,galGal2,xenTro1,danRer2,elephant,platypus,hedgehog,colobus_monkey,dusky_titi,owl_monkey,mouse_lemur"/>
|
|
<param name="split_blocks_by_species" value="dont_split_blocks_by_species"/>
|
|
<output name="out_file1" file="fsa_interval2maf.dat" />
|
|
</test>
|
|
<test>
|
|
<param name="input1" value="1.bed"/>
|
|
<param name="maf_source" value="user"/>
|
|
<param name="mafFile" value="fsa_interval2maf.dat"/>
|
|
<param name="species" value="hg17,panTro1,baboon,marmoset,galago,rn3,mm6,rabbit,cow,canFam1,rfbat,shrew,armadillo,tenrec,monDom1,tetNig1,fr1,rheMac1,galGal2,xenTro1,danRer2,elephant,platypus,hedgehog,colobus_monkey,dusky_titi,owl_monkey,mouse_lemur"/>
|
|
<param name="split_blocks_by_species" value="dont_split_blocks_by_species"/>
|
|
<output name="out_file1" file="fsa_interval2maf.dat" />
|
|
</test>
|
|
<test>
|
|
<param name="input1" value="1.bed" dbkey="hg18" ftype="bed"/>
|
|
<param name="maf_source" value="cached"/>
|
|
<param name="mafType" value="28_WAY_MULTIZ_hg18"/>
|
|
<param name="species" value="hg18,panTro2,mm8"/>
|
|
<param name="split_blocks_by_species" value="dont_split_blocks_by_species"/>
|
|
<output name="out_file1" file="interval2maf_3from28way.maf" />
|
|
</test>
|
|
</tests>
|
|
<help>
|
|
**What it does**
|
|
|
|
This tool takes genomic coordinates, superimposes them on multiple alignments (in MAF format) stored on the Galaxy site or from your history, and excises alignment blocks corresponding to each set of coordinates. Alignment blocks that extend past START and/or END positions of an interval are trimmed. Note that a single genomic interval may correspond to two or more alignment blocks.
|
|
|
|
-----
|
|
|
|
**Example**
|
|
|
|
Here a single interval is superimposed on three MAF blocks. Blocks 1 and 3 are trimmed because they extend beyond boundaries of the interval:
|
|
|
|
.. image:: ../static/images/maf_icons/interval2maf.png
|
|
|
|
</help>
|
|
</tool>
|