diff tools/extract/phastOdds/phastOdds_tool.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/extract/phastOdds/phastOdds_tool.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,67 @@
+<tool id="phastOdds_for_intervals" name="Compute phastOdds score" version="1.0.0">
+  <description>for each interval</description>
+  <command interpreter="python">get_scores_galaxy.py $per_col ${score_file}.h5 ${score_file}.mapping.bed $input $output ${input.metadata.chromCol} ${input.metadata.startCol} ${input.metadata.endCol}</command>
+  <inputs>
+    <param format="interval" name="input" type="data" label="Interval file">
+      <validator type="unspecified_build" message="Unspecified build, this tool works with data from genome builds hg17. Click the pencil icon in your history item to set the genome build."/>
+      <validator type="dataset_metadata_in_file" filename="phastOdds.loc" metadata_name="dbkey" metadata_column="0" message="Sequences are currently unavailable for the specified build." />
+    </param>
+    <param name="score_file" type="select" label="Available datasets">
+      <options from_file="phastOdds.loc">
+        <column name="name" index="1"/>
+        <column name="value" index="2"/>
+        <column name="dbkey" index="0"/>
+        <filter type="data_meta" ref="input" key="dbkey" column="0" />
+      </options>
+    </param>
+	<param name="per_col" type="boolean" label="Standardize" help="Standardizes the score to be per alignment column" checked="yes" truevalue="-p" falsevalue=""/>
+  </inputs>
+  <outputs>
+    <data format="interval" name="output" metadata_source="input"/>
+  </outputs>
+  <requirements>
+    <requirement type="python-module">numpy</requirement>
+    <requirement type="python-module">tables</requirement>
+  </requirements>
+  <tests>
+    <test>
+      <param name="input" value="4.bed" dbkey="hg17" ftype="bed"/>
+      <param name="score_file" value="/galaxy/data/phastOdds_precomputed/encode_SEP-2005_tba.v2_phastOdds" />
+      <param name="per_col" value="true" />
+      <output name="output" file="phastOdds_tool_out.interval" />
+    </test>
+  </tests>
+  <help>
+    
+.. class:: warningmark
+
+This tool currently only works with interval data from genome build hg17.
+
+.. class:: warningmark
+
+This tool assumes that the input dataset is in interval format and contains at least a chrom column, a start column and an end column.  These 3 columns can be dispersed throughout any number of other data columns. 
+
+-----
+
+**Syntax**
+
+Append a column to each line of an interval file containing the phastOdds score for that interval.
+
+-----
+
+**Example**
+
+If your original data has the following format:
+
++-----+-----+---+
+|chrom|start|end|
++-----+-----+---+
+
+and you choose to compute phastOdds scores, your output will look like this:
+
++-----+-----+---+-----+
+|chrom|start|end|score|
++-----+-----+---+-----+
+
+  </help>
+</tool>