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/tools/maf/interval_maf_to_merged_fasta.xml

https://bitbucket.org/cistrome/cistrome-harvard/
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  1<tool id="Interval_Maf_Merged_Fasta2" name="Stitch MAF blocks" version="1.0.1">
  2  <description>given a set of genomic intervals</description>
  3  <command interpreter="python">
  4    #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=${GALAXY_DATA_INDEX_DIR}
  5    #else                                     #interval_maf_to_merged_fasta.py --dbkey=$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}
  6    #end if# --overwrite_with_gaps=$overwrite_with_gaps
  7  </command>
  8  <inputs>
  9    <page>
 10        <param format="interval" name="input1" type="data" label="Choose intervals">
 11          <validator type="unspecified_build" />
 12        </param>
 13        <conditional name="maf_source_type">
 14            <param name="maf_source" type="select" label="MAF Source">
 15              <option value="cached" selected="true">Locally Cached Alignments</option>
 16              <option value="user">Alignments in Your History</option>
 17            </param>
 18            <when value="user">
 19              <param name="maf_file" type="data" format="maf" label="MAF File">
 20                <options>
 21                  <filter type="data_meta" ref="input1" key="dbkey" />
 22                </options>
 23                <validator type="dataset_ok_validator" />
 24              </param>
 25              <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
 26                <options>
 27                  <filter type="data_meta" ref="maf_file" key="species" />
 28                </options>
 29              </param>
 30            </when>
 31            <when value="cached">
 32              <param name="maf_identifier" type="select" label="MAF Type" >
 33                <options from_file="maf_index.loc">
 34                  <column name="name" index="0"/>
 35                  <column name="value" index="1"/>
 36                  <column name="dbkey" index="2"/>
 37                  <column name="species" index="3"/>
 38                  <filter type="data_meta" ref="input1" key="dbkey" column="2" multiple="True" separator=","/>
 39                  <validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/>
 40                </options>
 41              </param> 
 42              <param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment">
 43                <options from_file="maf_index.loc">
 44                  <column name="uid" index="1"/>
 45                  <column name="value" index="3"/>
 46                  <column name="name" index="3"/>
 47                  <filter type="param_value" ref="maf_identifier" name="uid" column="1"/>
 48                  <filter type="multiple_splitter" column="3" separator=","/>
 49                </options>
 50              </param>
 51            </when>
 52        </conditional>
 53        <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.">
 54          <option value="True" selected="true">No</option>
 55          <option value="False">Yes</option>
 56        </param>
 57    </page>
 58   </inputs>
 59  <outputs>
 60    <data format="fasta" name="out_file1" />
 61  </outputs>
 62  <tests>
 63    <test>
 64      <param name="input1" value="13.bed" dbkey="hg18" ftype="bed"/>
 65      <param name="maf_source" value="cached"/>
 66      <param name="maf_identifier" value="17_WAY_MULTIZ_hg18"/>
 67      <param name="species" value="hg18,mm8"/>
 68      <param name="overwrite_with_gaps" value="True"/>
 69      <output name="out_file1" file="interval_maf_to_merged_fasta_out3.fasta" />
 70    </test>
 71    <test>
 72      <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/>
 73      <param name="maf_source" value="cached"/>
 74      <param name="maf_identifier" value="8_WAY_MULTIZ_hg17"/>
 75      <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/>
 76      <param name="overwrite_with_gaps" value="True"/>
 77      <output name="out_file1" file="interval_maf_to_merged_fasta_out.dat" />
 78    </test>
 79    <test>
 80      <param name="input1" value="1.bed" dbkey="hg17" ftype="bed"/>
 81      <param name="maf_source" value="user"/>
 82      <param name="maf_file" value="5.maf"/>
 83      <param name="species" value="canFam1,hg17,mm5,panTro1,rn3"/>
 84      <param name="overwrite_with_gaps" value="True"/>
 85      <output name="out_file1" file="interval_maf_to_merged_fasta_user_out.dat" />
 86    </test>
 87  </tests>
 88  <help>
 89**What it does**
 90
 91A 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:
 92
 93  * finds all MAF blocks that overlap the interval;
 94  * sorts MAF blocks by alignment score;
 95  * stitches blocks together and resolves overlaps based on alignment score;
 96  * outputs alignments in FASTA format.
 97
 98------
 99
100**Example**
101
102Here three MAF blocks overlapping a single interval are stitched together. Space between blocks 2 and 3 is filled with gaps:
103
104.. image:: ${static_path}/images/maf_icons/stitchMaf.png
105
106------
107
108**Citation**
109
110If 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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21775304&gt;`_
111
112
113  </help>
114</tool>