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. &lt;http://www.ncbi.nlm.nih.gov/pubmed/21775304&gt;`_
+
+
+  </help>
+</tool>