diff macs2_filterdup.xml @ 0:fe62ba547975 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macs2_filterdup.xml	Wed Feb 11 10:18:02 2015 -0500
@@ -0,0 +1,57 @@
+<tool id="macs2_filterdup" name="MACS2 filterdup" version="@VERSION_STRING@.0">
+    <description>Remove duplicate reads at the same position</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>macs2_macros.xml</import>
+    </macros>
+    <command>
+        macs2 filterdup
+            -i "${ infile }"
+            -o temp_outfile
+
+        --format '${ infile.extension.upper() }'
+        @effective_genome_size@
+        @tag_size@
+        --pvalue "${ pvalue }"
+        #if str( $keep_dup_options.keep_dup_options_selector ) == "user":
+            --keep-dup "${ keep_dup_options.user_keepdup }"
+        #else
+            --keep-dup "${ keep_dup_options.keep_dup_options_selector }"
+        #end if
+	;
+	mv temp_outfile "${ outfile }"
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
+        <expand macro="conditional_effective_genome_size" />
+        <expand macro="tag_size" />
+        <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="default: 1e-5 (--pvalue)" />
+
+        <expand macro="keep_duplicates" />
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="ChIP_200K_w_dups.bed" ftype="bed"/>
+            <param name="pvalue" value="1e-5"/>
+            <param name="keep_dup_options_selector" value="auto"/>
+            <param name="effective_genome_size_options_selector" value="user_defined" />
+            <param name="gsize" value="3300000000" />
+            <output name="outfile" file="filterdup_on_ChIP_200K_w_dups.bed"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Remove duplicate reads at the same position, then convert acceptable format to BED format.
+filterdup tool from macs2
+
+@citation@
+  </help>
+  <expand macro="citations" />
+</tool>