diff peptideGenomicCoodinate.xml @ 4:b56922070a1b draft default tip

planemo upload

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/peptideGenomicCoodinate.xml	Tue Dec 18 16:22:29 2018 -0500
@@ -0,0 +1,56 @@
+<tool id="peptidegenomiccoodinate" name="Peptide Genomic Coodinate" version="0.1.1">
+    <description>Get genomic location/coordinate of peptides using mzsqlite DB and genomic mapping sqlite DB</description>
+    <requirements>
+        <requirement type="package" version="2.7.9">python</requirement>
+        <!--<requirement type="package" version="3.26.0">sqlite</requirement>-->
+    </requirements>
+    <command detect_errors="aggressive"><![CDATA[
+        python '$__tool_directory__/peptideGenomicCoodinate.py' 
+        '$peptideinput'
+        '$mzsqlite'
+        '$mapping'
+        '$peptide_bed'
+    ]]></command>
+    <inputs>
+        <param type="data" name="peptideinput" format="tabular" label="Peptide List (without any header line)"/>
+        <param type="data" name="mzsqlite" format="sqlite" label="mz to sqlite (mzsqlite) file"/>
+        <param type="data" name="mapping" format="sqlite" label="genomic mapping sqlite file"/>
+    </inputs>
+    <outputs>
+        <data format="bed" name="peptide_bed" label="${tool.name} on ${on_string}">
+            <actions>
+                <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts"/>
+            </actions>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="peptideinput" value="peptides.tabular"/>
+            <param name="mzsqlite" value="test_mz_to_sqlite.sqlite"/>
+            <param name="mapping" value="test_genomic_mapping_sqlite.sqlite"/>
+            <output name="peptide_bed">
+                <assert_contents>
+                    <has_text text="115176449" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+        **PeptideGenomicCoodinate**
+        Gets genomic coordinate of peptides based on the information in mzsqlite and genomic mapping sqlite files. This tool is useful in a proteogenomics workflow.
+        This program loads two sqlite databases (mzsqlite and genomic mapping sqlite files) and calculates the genomic coordinates of the peptides provided as input. This outputs bed file for peptides.
+    
+        Input: Peptide list file, mzsqlite sqlite DB file, and genomic mapping sqlite DB file 
+        Output: Tabular BED file with all the columns
+        
+    ]]></help>
+    <citations>
+      <citation type="bibtex">
+@misc{peptidegenomiccoodinate,
+    author={Kumar, Praveen},
+    year={2018},
+    title={PeptideGenomicCoordinate}
+}
+      </citation>
+    </citations>
+</tool>