diff DimontDataExtractor.xml @ 11:fa520092c603 draft

Uploaded

--- a/DimontDataExtractor.xml	Thu Nov 07 15:17:42 2013 -0500
+++ b/DimontDataExtractor.xml	Thu Nov 07 16:59:25 2013 -0500
@@ -1,21 +1,21 @@
-<tool id="DimontDataExtractor" name="Dimont Data Extractor" version="0.1" force_history_refresh="true">
+<tool id="DimontDataExtractor" name="Dimont Data Extractor" version="0.1">
 <description>Extracts genomic regions specified in a BED-like file format in the annotated FastA format as required by Dimont</description>
-<command interpreter="perl">extract_data_single_galaxy.pl $genomefa $regions $chromcol $startcol $seccol $seccoord $width $statcol extracted.fa</command>
+<command interpreter="perl">extract_data_single_galaxy.pl $genomefa $regions $chromcol $startcol $seccol $seccoord $width $statcol $extracted</command>
 <inputs>
 	<param type="data" format="bed,gtf,txt,tabular" name="regions" label="Genomic regions" value="" optional="false" help="The genomic regions to be extracted in a BED-like file format, e.g., BED, GTF, narrowPeak." />
 	<param type="data" format="fasta" name="genomefa" label="Genome sequence" value="" optional="false" help="The input genome to which the genomic regions refer." />
-	<param type="integer" name="chromcol" label="Chromosome column" value="1" optional="false" help="The column of the regions file, which contains the chromosome information." />
-	<param type="integer" name="startcol" label="Start column" value="2" optional="false" help="The column of the Regions file containing the start position of the genomic region." />
+	<param type="data_column" data_ref="regions" force_select="true" name="chromcol" label="Chromosome column" value="1" optional="false" help="The column of the regions file, which contains the chromosome information." />
+	<param type="data_column" data_ref="regions" force_select="true" name="startcol" label="Start column" value="2" optional="false" help="The column of the Regions file containing the start position of the genomic region." />
 	<param type="select" name="seccol" label="Meaning of second coordinate" optional="false" help="The meaning of the second genomic coordinate. This may either be the position of the peak summit relative to the position in Start, or the end position of the peak.">
 		<option value="end">End of peak (in global coordinates)</option>
 		<option value="center">Center of peak (relative to start)</option>
 	</param>
-	<param type="integer" name="seccoord" label="Second coordinate" value="3" optional="false" help="The second genomic coordinate with meaning specified by parameter &quot;Meaning of second coordinate&quot;" />
-	<param type="integer" name="statcol" label="Statistics column" value="7" optional="false" help="The column containing the peak statistics information (or another measure of peak confidence)." />
+	<param type="data_column" data_ref="regions" force_select="true" name="seccoord" label="Second coordinate" value="3" optional="false" help="The second genomic coordinate with meaning specified by parameter &quot;Meaning of second coordinate&quot;" />
+	<param type="data_column" data_ref="regions" force_select="true" name="statcol" label="Statistics column" value="7" optional="false" help="The column containing the peak statistics information (or another measure of peak confidence)." />
 	<param type="integer" name="width" label="Width" value="1000" optional="false" help="The width of the genomic region to be extracted. Recommended values: 1000 for ChIP-seq and 100 for ChIP-exo." />
 </inputs>
 <outputs>
-	<data format="fasta" name="extracted.fa">
+	<data format="fasta" name="extracted">
 	</data>
 </outputs>
 <tests>
@@ -28,7 +28,7 @@
 		<param name="seccoord" value="3" />
 		<param name="statcol" value="7" />
 		<param name="width" value="200" />
-		<output name="extracted.fa" file="mini_extracted.fa" /> 
+		<output name="extracted" file="mini_extracted.fa" /> 
 	</test>
 	<test>
 		<param name="regions" value="mini2.bed" />
@@ -39,7 +39,7 @@
 		<param name="seccoord" value="3" />
 		<param name="statcol" value="7" />
 		<param name="width" value="200" />
-		<output name="extracted.fa" file="mini2_extracted.fa" /> 
+		<output name="extracted" file="mini2_extracted.fa" /> 
 	</test>
 </tests>
 <help>