changeset 0:aedc582b98aa draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_custom_track/construct_custom_track.py	Fri Sep 23 13:11:37 2022 +0000
@@ -0,0 +1,18 @@
+import sys
+
+def main(track_type, url, sample_name, sample_description, chromosome_position, outpath):
+    
+    with open(outpath, 'w') as f:
+        f. write(f"""
+        browser position {chromosome_position}
+        track type={track_type} name="{sample_name}" description="{sample_description}" bigDataUrl={url}
+        """)
+
+if __name__ == "__main__":
+    track_type = sys.argv[1]
+    url = sys.argv[2]
+    sample_name = sys.argv[3]
+    sample_description = sys.argv[4]
+    chromosome_position = sys.argv[5]
+    outpath = sys.argv[6]
+    main(track_type, url, sample_name, sample_description, chromosome_position, outpath)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_custom_track/generate_custom_track.xml	Fri Sep 23 13:11:37 2022 +0000
@@ -0,0 +1,35 @@
+<tool id="generate-custom_track" name="Generate Custom Track" version="0.1">
+    <description>Generates a Custom Track File for GWIPS-viz.</description>
+    <command>
+    python construct_custom_track.py $input1 $input2 "$input3" "$input4"
+    </command>
+
+    <inputs>
+        <param name="input1" type="select" label="File Type">
+            <option value="bigWig" selected="True">bigWig</option>
+            <option value="bigBed">bigBed</option>
+        </param>
+        <param name="input2" type="text" label="URL of File (copy link from history)" />
+        <param name="input3" type="text" label="Name of this sample" />
+        <param name="input4" type="text" label="Description of this sample" />
+        <param name="input5" type="text" label="chromosome position" help="Get this from Gwips.ucc.ie. Hg38 example = chr9:136,848,259-136,851,600"/>
+    </inputs>
+    <outputs>
+       <data name="output1" format="text"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="test.fasta" ftype="fasta" />
+            <param name="input2" value="chr"/>
+            <output name="output1" file="test.fasta.sizes" ftype="tabular" lines_diff="4" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Generates a custom track file for GWIPS-viz. 
+
+This is facilitates easy exploration of data processed on RiboGalaxy at a Genome wide scale.
+    </help>
+    <citations/>
+</tool>
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