# HG changeset patch
# User kevyin
# Date 1353648604 18000
# Node ID 59d58008c40d2712d213fad4585c015c838af1e8
# Parent  2103c773690f98643f38bde2bc5f791ea54f694c
Deleted selected files

diff -r 2103c773690f -r 59d58008c40d annotatePeaks.xml
--- a/annotatePeaks.xml	Fri Nov 09 00:53:35 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,41 +0,0 @@
-<tool id="homer_annotatePeaks" name="homer_annotatePeaks" version="0.0.2">
-    <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; $out_log || echo "Error running annotatePeaks." >&amp;2
-    </command>
-    <inputs>
-        <param format="tabular,bed" name="input_bed" type="data" label="Homer peak positions or BED format" />
-        <param name="genome_selector" type="select" label="Genome version">
-            <option value="hg19" selected="true">hg19</option>
-        </param>
-    </inputs>
-    <outputs>
-        <!--<data format="html" name="html_outfile" label="index" />-->
-        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
-        <data format="csv" name="out_annotated" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}" />
-        <data format="txt" name="out_log" label="${tool.name} on #echo os.path.splitext(str($input_bed.name))[0]#_genome_${genome_selector}.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>
-
diff -r 2103c773690f -r 59d58008c40d bed2pos.xml
--- a/bed2pos.xml	Fri Nov 09 00:53:35 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-<tool id="homer_bed2pos" name="homer_bed2pos" version="0.0.2">
-    <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>
-
diff -r 2103c773690f -r 59d58008c40d pos2bed.xml
--- a/pos2bed.xml	Fri Nov 09 00:53:35 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-<tool id="homer_pos2bed" name="homer_pos2bed" version="0.0.2">
-    <requirements>
-        <requirement type="package">homer</requirement>
-    </requirements>
-    <description></description>
-    <!--<version_command></version_command>-->
-    <command>
-        pos2bed.pl $input_peak 1&gt; $out_bed
-        2&gt; $out_log || echo "Error running pos2bed." >&amp;2
-    </command>
-    <inputs>
-        <param format="tabular" name="input_peak" type="data" label="Homer peak positions" />
-    </inputs>
-    <outputs>
-        <!--<data format="html" name="html_outfile" label="index" />-->
-        <!--<data format="html" hidden="True" name="html_outfile" label="index.html" />-->
-        <data format="bed" name="out_bed" label="${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>
-