diff tools/maf/maf_stats.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/maf/maf_stats.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,120 @@
+<tool id="maf_stats1" name="MAF Coverage Stats" version="1.0.1">
+  <description>Alignment coverage information</description>
+  <command interpreter="python">
+    maf_stats.py
+    #if $maf_source_type.maf_source == "user":
+      $maf_source_type.maf_source $input2 $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary
+    #else:
+      $maf_source_type.maf_source $maf_source_type.mafType $input1 $out_file1 $dbkey ${input1.metadata.chromCol} ${input1.metadata.startCol} ${input1.metadata.endCol} $summary
+    #end if
+    ${GALAXY_DATA_INDEX_DIR}
+    #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="MAF File" type="data">
+          <options>
+            <filter type="data_meta" ref="input1" key="dbkey" />
+          </options>
+          <validator type="dataset_ok_validator" />
+        </param>
+      </when>
+      <when value="cached">
+        <param name="mafType" 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"/>
+            <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> 
+      </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>
+  <requirements>
+    <requirement type="python-module">numpy</requirement>
+  </requirements>
+  <tests>
+    <test>
+      <param name="input1" value="1.bed" dbkey="hg17" format="bed"/>
+      <param name="maf_source" value="cached"/>
+      <param name="mafType" value="8_WAY_MULTIZ_hg17"/>
+      <output name="out_file1" file="maf_stats_interval_out.dat"/>
+      <param name="summary" value="false"/>
+    </test>
+    <test>
+      <param name="input1" value="1.bed" dbkey="hg17" format="bed"/>
+      <param name="maf_source" value="cached"/>
+      <param name="mafType" value="8_WAY_MULTIZ_hg17"/>
+      <output name="out_file1" file="maf_stats_summary_out.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.
+
+------
+
+**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>