changeset 1:f252cf28746d draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/crossmap.xml	Wed Jul 22 08:20:16 2015 -0400
@@ -0,0 +1,71 @@
+<tool id="crossmap" name="crossmap" version="0.1.8">
+    <description>Convert genome coordinates or annotation files between genome assemblies</description>
+    
+    <requirements>
+        <requirement type="package" version="0.1.8">crossmap</requirement>
+    </requirements>
+    
+    <stdio></stdio>
+
+    <command>
+        CrossMap.py --help > $output
+    </command>
+
+    <inputs>
+        <param format="interval,gff,gtf,vcf" name="input" type="data" label="Convert coordinates of" />
+        <!--
+        <param format="interval,gff,gtf,vcf" name="input" type="data" label="Convert coordinates of">
+            <validator type="unspecified_build" />
+            <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." />
+        </param>
+        <param name="to_dbkey" type="select" label="To">
+            <options from_file="liftOver.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="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" help="Recommended values: same species = 0.95, different species = 0.10" />
+        <conditional name="multiple">
+                <param name="choice" type="select" label="Allow multiple output regions?" help="Recommended values: same species = No, different species = Yes">
+                        <option value="0" selected="true">No</option>
+                        <option value="1">Yes</option>
+                </param>
+                <when value="0">
+                        <param name="minSizeQ" type="hidden" value="0" />
+                        <param name="minChainQ" type="hidden" value="0" />
+                        <param name="minChainT" type="hidden" value="0" />
+                </when>
+                <when value="1">
+                        <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in dataset" help="Recommended value: set to >= 300 bases for complete transcripts"/>
+                        <param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in dataset"/>
+                        <param name="minChainT" size="10" type="integer" value="500" label="Minimum chain size in target"/>
+                </when>
+        </conditional>
+        -->
+    </inputs>
+    
+    <outputs>
+        <data format="text" name="output" label="Output file">
+        </data>
+    </outputs>
+    
+    <tests>
+        <test>
+            <param name="input" value="test1.hg19.txt"/>
+            <output name="output" file="test1.hg18.txt"/>
+        </test>
+    </tests>
+    
+    <help>
+        CrossMap is versatile tool to convert genome coordinates or annotation files between genome
+assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF,
+GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF
+and VCF, reading from remote servers and file compression are supported.
+    </help>
+    
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btt730</citation>
+    </citations>
+</tool>