--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/homer_scanMotifGenomeWide.xml	Mon Dec 13 15:13:33 2021 +0000
@@ -0,0 +1,94 @@
+<tool id="homer_scanMotifGenomeWide" name="scanMotifGenomeWide" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05" license="MIT">
+    <description/>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="xrefs"/>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+scanMotifGenomeWide.pl
+'$motif'
+#if str( $genome.source ) == "installed":
+    '$genome.all_fasta_source.fields.path'
+#elif str( $genome.source ) == "history":
+    '$genome.fasta'
+#end if
+$bed
+$keepAll
+$mask
+$Fivep
+$homer1
+> 
+#if $bed:
+    '${output_bed}'
+#else
+    '${output_text}'
+#end if
+        ]]></command>
+    <inputs>
+        <param name="motif" type="data" format="txt" label="Motif file"/>
+        <conditional name="genome">
+            <param name="source" type="select" label="Will you select a reference genome from your history or use a installed genome?">
+                <option value="installed">Installed</option>
+                <option value="history">From History</option>
+            </param>
+            <when value="installed">
+                <param name="all_fasta_source" type="select" label="Source FASTA Sequence">
+                    <options from_data_table="all_fasta">
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="No references are available"/>
+                    </options>
+                </param>
+            </when>
+            <when value="history">
+                <param name="fasta" type="data" format="fasta" label="Select reference genome"/>
+            </when>
+        </conditional>
+        <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false" label="Output bed format"/>
+        <param argument="-keepAll" type="boolean" truevalue="-keepAll" falsevalue="" checked="false" label="Report all motifs even if overlap"
+        help="By default, HOMER will remove a motif that overlaps itself, useful for palindromes. To report all, specify this option."/>
+        <param argument="-mask" type="boolean" truevalue="-mask" falsevalue="" checked="false"
+        label="Do not look for motifs in RepeatMasked sequence (lower case sequence in FASTA files)"/>
+        <param argument="-5p" name="Fivep" type="boolean" truevalue="-5p" falsevalue="" checked="false"
+        label="Report motif positions based on the 5' end of the motif sequence"/>
+        <param argument="-homer1" type="boolean" truevalue="-homer1" falsevalue="" checked="false"
+        label="Use homer1 instead of homer2"/>
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output_text" label="${tool.name} on ${on_string}">
+            <filter>bed is False</filter>
+        </data>
+        <data format="bed" name="output_bed" label="${tool.name} on ${on_string}">
+            <filter>bed is True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="motif" value="motif_test1/homerResults/motif1.motif"/>
+            <conditional name="genome">
+                <param name="source" value="installed"/>
+                <param name="all_fasta_source" value="phiX174"/>
+            </conditional>
+            <output name="output_text" file="scanMotif_res1.txt" ftype="tabular"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="motif" value="motif_test1/homerResults/motif1.motif"/>
+            <conditional name="genome">
+                <param name="source" value="history"/>
+                <param name="fasta" value="phiX174.fasta"/>
+            </conditional>
+            <param name="bed" value="-bed"/>
+            <output name="output_bed" file="scanMotif_res1.bed" ftype="bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+    This is a wrapper for scanMotifGenomeWide.pl from HOMER but not all options are included.
+
+    The scanMotifGenomeWide.pl script will take a motif file (may contain multiple motifs) and look for instances across the genome. 
+
+    ]]></help>
+    <expand macro="citation"/>
+</tool>