Mercurial > repos > xuebing > sharplabtool
diff tools/maf/interval_maf_to_merged_fasta.xml @ 0:9071e359b9a3
Uploaded
| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/maf/interval_maf_to_merged_fasta.xml Fri Mar 09 19:37:19 2012 -0500 @@ -0,0 +1,114 @@ +<tool id="Interval_Maf_Merged_Fasta2" name="Stitch MAF blocks" version="1.0.1"> + <description>given a set of genomic intervals</description> + <command interpreter="python"> + #if $maf_source_type.maf_source == "user" #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_file --mafIndex=$maf_source_type.maf_file.metadata.maf_index --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} + #else #interval_maf_to_merged_fasta.py --dbkey=$dbkey --species=$maf_source_type.species --mafSource=$maf_source_type.maf_identifier --interval_file=$input1 --output_file=$out_file1 --chromCol=${input1.metadata.chromCol} --startCol=${input1.metadata.startCol} --endCol=${input1.metadata.endCol} --strandCol=${input1.metadata.strandCol} --mafSourceType=$maf_source_type.maf_source --mafIndexFileDir=${GALAXY_DATA_INDEX_DIR} + #end if# --overwrite_with_gaps=$overwrite_with_gaps + </command> + <inputs> + <page> + <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 name="maf_file" type="data" format="maf" label="MAF File"> + <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="maf_file" key="species" /> + </options> + </param> + </when> + <when value="cached"> + <param name="maf_identifier" type="select" label="MAF Type" > + <options from_file="maf_index.loc"> + <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="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_file="maf_index.loc"> + <column name="uid" index="1"/> + <column name="value" index="3"/> + <column name="name" index="3"/> + <filter type="param_value" ref="maf_identifier" name="uid" column="1"/> + <filter type="multiple_splitter" column="3" separator=","/> + </options> + </param> + </when> + </conditional> + <param name="overwrite_with_gaps" type="select" label="Split into Gapless MAF blocks" help="When set to Yes, blocks are divided around gaps appearing in any species. This will prevent gaps occurring in the interior of the sequence for an aligning species from overwriting a nucleotide found for the same position in a lower-scoring block."> + <option value="True" selected="true">No</option> + <option value="False">Yes</option> + </param> + </page> + </inputs> + <outputs> + <data format="fasta" name="out_file1" /> + </outputs> + <tests> + <test> + <param name="input1" value="13.bed" dbkey="hg18" ftype="bed"/> + <param name="maf_source" value="cached"/> + <param name="maf_identifier" value="17_WAY_MULTIZ_hg18"/> + <param name="species" value="hg18,mm8"/> + <param name="overwrite_with_gaps" value="True"/> + <output name="out_file1" file="interval_maf_to_merged_fasta_out3.fasta" /> + </test> + <test> + <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/> + <param name="maf_source" value="cached"/> + <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/> + <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> + <param name="overwrite_with_gaps" value="True"/> + <output name="out_file1" file="interval_maf_to_merged_fasta_out.dat" /> + </test> + <test> + <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/> + <param name="maf_source" value="user"/> + <param name="maf_file" value="5.maf"/> + <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/> + <param name="overwrite_with_gaps" value="True"/> + <output name="out_file1" file="interval_maf_to_merged_fasta_user_out.dat" /> + </test> + </tests> + <help> +**What it does** + +A single genomic region can be covered by multiple alignment blocks. In many cases it is desirable to stitch these alignment blocks together. This tool accepts a list of genomic intervals. For every interval it performs the following: + + * finds all MAF blocks that overlap the interval; + * sorts MAF blocks by alignment score; + * stitches blocks together and resolves overlaps based on alignment score; + * outputs alignments in FASTA format. + +------ + +**Example** + +Here three MAF blocks overlapping a single interval are stitched together. Space between blocks 2 and 3 is filled with gaps: + +.. image:: ./static/images/maf_icons/stitchMaf.png + +------ + +**Citation** + +If you use this tool, please cite `Blankenberg D, Taylor J, Nekrutenko A; The Galaxy Team. Making whole genome multiple alignments usable for biologists. Bioinformatics. 2011 Sep 1;27(17):2426-2428. <http://www.ncbi.nlm.nih.gov/pubmed/21775304>`_ + + + </help> +</tool>