--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/manhattan_plot.xml	Fri Oct 11 17:31:09 2019 -0400
@@ -0,0 +1,88 @@
+<tool id="gwastools_manhattan_plot" name="Manhattan plot" version="0.1.0" python_template_version="3.5">
+    <description>Generate plots for use with GWAS pipelines</description>
+    <requirements>
+        <requirement type="package" version="3.6">r-base</requirement>
+        <requirement type="package" version="1.30.0">bioconductor-gwastools</requirement>
+        <requirement type="package" version="1.6.4">r-optparse</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript '$__tool_directory__/manhattan.R'
+        --file '${file}'
+        --pval ${pvals}
+        --chromosome ${chromosome}
+        #if $ymax:
+            --ymax ${ymax}
+        #end if
+        #if $ymin:
+            --ymin ${ymin}
+        #end if
+        ${trunc}
+        #if $sig:
+            --sig ${sig}
+        #end if
+        #if $thinselect.thinning == 'Yes':
+            --thin ${thinselect.thin}
+            #if $thinselect.ppb:
+                --ppb ${thinselect.ppb}
+            #end if
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="file" type="data" format="tsv,tabular" label="GWAS data file"/>
+        <param name="chromosome" type="data_column" data_ref="file" label="Chromosome column number"/>
+        <param name="pvals" type="data_column" data_ref="file" label="P-values column number"/>
+        <param name="ymax" type = "float" optional="true" label="Y max"/>
+        <param name="ymin" type = "float" optional="true" label="Y min"/>
+        <param name="trunc" type="boolean" truevalue="--trunc" falsevalue="" label="Show truncation lines?"/>
+        <param name="sig" type="float" optional="true" label="Genome-wide significance level for plotting horizontal line." help="If not specified, no line will be drawn."/>
+        <conditional name="thinselect">
+            <param name="thinning" type="select" label='Specify thinning value?'>
+                <option value="Yes"/>
+                <option value="No"/>
+            </param>
+            <when value="Yes">
+                <param name="thin" type="float" value="0" label="Threshold for thinning points" help="If not specified, value is -log10(val)"/>
+                <param name="ppb" type="integer" optional="true" label="Points per bin"/>
+            </when>
+            <when value="No"/>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="manhattanout" format="pdf" from_work_dir="manhattan.pdf" label="Manhattan plot on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="file" value="sampledata.tsv"/>
+            <param name="chromosome" value="2"/>
+            <param name="pvals" value="4"/>
+            <param name="ymin" value="0.2"/>
+            <param name="trunc" value="--trunc"/>
+            <param name="ymax" value="2"/>
+            <param name="sig" value="0.05"/>
+            <conditional name="thinselect">
+                <param name="thinning" value="yes"/>
+                <param name="thin" value="1"/>
+                <param name="ppb" value="1"/>
+            </conditional>
+            <output name="manhattanout" ftype="pdf" value="testgraph.pdf" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Generates a manhattan plot for GWAS data
+
+        Input data format example:
+
+            SNP CHR  Pos  P
+            rs1   1  1 0.9148
+            rs2   1  2 0.9371
+            rs3   1  3 0.2861
+            rs4   1  4 0.8304
+            rs5   1  5 0.6417
+            rs6   1  6 0.5191
+            rs16468  22 533 0.1779
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/bts610</citation>
+    </citations>
+</tool>