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changeset 13:106c7c3720aa draft

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Uploaded
author kevyin
date Wed, 07 Nov 2012 01:03:51 -0500
parents 1bce61936d45
children 64d206abd8bc
files annotatePeaks.xml bed2pos.xml pos2bed.xml
diffstat 3 files changed, 68 insertions(+), 41 deletions(-) [+]
line wrap: on
line diff
--- a/annotatePeaks.xml	Thu Nov 01 23:05:53 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-<tool id="homer-annotate-peaks" name="annotate-peaks" version="0.0.1">
-    <requirements>
-        <requirement type="package">homer</requirement>
-    </requirements>
-    <description></description>
-    <!--<version_command></version_command>-->
-    <command>
-        annotatePeaks.pl $input_bed $genome_selector 1&gt; $out_annotated
-        2&gt; $out_log || echo "Error running annotatePeaks." >&amp;2
-    </command>
-    <inputs>
-        <param format="tabular,bed" name="input_bed" type="data" label="Intervals in BED format" />
-        <param name="genome_selector" type="select" label="Genome version">
-            <option value="hg19" selected="true">hg19</option>
-        </param>
-    </inputs>
-    <outputs>
-        <!--<data format="html" name="html_outfile" label="index" />-->
-        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
-        <data format="csv" name="out_annotated" label="Annotated" />
-        <data format="txt" name="out_log" label="homer_annotatePeaks.log" />
-    </outputs>
-    <tests>
-        <test>
-            <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
-            <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
-        </test>
-    </tests>
-
-    <help>
-
-        .. class:: infomark
-
-        **Homer annoatePeaks**
-        More information on accepted formats
-        http://biowhat.ucsd.edu/homer/ngs/annotation.html
-
-
-    </help>
-</tool>
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bed2pos.xml	Wed Nov 07 01:03:51 2012 -0500
@@ -0,0 +1,34 @@
+<tool id="homer_bed2pos" name="homer_bed2pos" version="0.0.1">
+    <requirements>
+        <requirement type="package">homer</requirement>
+    </requirements>
+    <description></description>
+    <!--<version_command></version_command>-->
+    <command>
+        bed2pos.pl $input_bed 1&gt; $out_pos
+        2&gt; $out_log || echo "Error running bed2pos." >&amp;2
+    </command>
+    <inputs>
+        <param format="tabular,bed" name="input_bed" type="data" label="BED file" />
+    </inputs>
+    <outputs>
+        <!--<data format="html" name="html_outfile" label="index" />-->
+        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
+        <data format="tabular" name="out_pos" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#" />
+        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#.log" />
+    </outputs>
+    <tests>
+        <test>
+            <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
+            <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
+        </test>
+    </tests>
+
+    <help>
+        .. class:: infomark
+
+        **Homer bed2pos.pl**
+        http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html
+    </help>
+</tool>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pos2bed.xml	Wed Nov 07 01:03:51 2012 -0500
@@ -0,0 +1,34 @@
+<tool id="homer_pos2bed" name="homer_pos2bed" version="0.0.1">
+    <requirements>
+        <requirement type="package">homer</requirement>
+    </requirements>
+    <description></description>
+    <!--<version_command></version_command>-->
+    <command>
+        pos2bed.pl $input_peak 1&gt; $out_bed
+        2&gt; $out_log || echo "Error running pos2bed." >&amp;2
+    </command>
+    <inputs>
+        <param format="tabular" name="input_peak" type="data" label="Homer peak positions" />
+    </inputs>
+    <outputs>
+        <!--<data format="html" name="html_outfile" label="index" />-->
+        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
+        <data format="bed" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.bed" />
+        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_peak.name))[0]#.log" />
+    </outputs>
+    <tests>
+        <test>
+            <!--<param name="input_file" value="extract_genomic_dna.fa" />-->
+            <!--<output name="html_file" file="sample_output.html" ftype="html" />-->
+        </test>
+    </tests>
+
+    <help>
+        .. class:: infomark
+
+        **Homer pos2bed.pl**
+        http://biowhat.ucsd.edu/homer/ngs/miscellaneous.html
+    </help>
+</tool>
+