diff data_manager/data_manager_snpsift_dbnsfp.xml @ 0:0e9e3bb5776a draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_snpsift_dbnsfp commit 5316af00b4a71a7b526cbc9540d5158749cc38e4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_snpsift_dbnsfp.xml	Tue Jun 07 10:23:16 2016 -0400
@@ -0,0 +1,89 @@
+<tool id="data_manager_snpsift_dbnsfp" name="SnpSift dbNSFP" version="4.1.0" tool_type="manage_data">
+    <description>Install a dbNSFP variant annotation database</description>
+    <requirements>
+        <requirement type="package" version="0.7.7">pysam</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+        <exit_code range="1:"  level="fatal"   description="Error" />
+    </stdio>
+    <command interpreter="python">
+        #import re
+        data_manager_snpsift_dbnsfp.py 
+        #if $db.src == 'softgenetics':
+            --softgenetics "$db.softgenetics_name"
+        #elif $db.src == 'history':
+            #if $db.snpsiftdbnsfp.ext == 'snpsiftdbnsfp':
+                #import os.path
+                --snpsiftdbnsfp "$os.path.join($db.snpsiftdbnsfp.extra_files_path, $db.snpsiftdbnsfp.metadata.bgzip)"
+            #else 
+                --dbnsfp_tabular "$db.snpsiftdbnsfp"
+            #end if
+            --db_name "$db.db_name"
+            #if str($db.dbkey).strip() != '': 
+                --dbkey "$db.dbkey" 
+            #elif str($db.snpsiftdbnsfp.metadata.dbkey) != '?':
+                --dbkey "$db.snpsiftdbnsfp.metadata.dbkey" 
+            #end if
+        #end if
+        "$out_file"
+        </command>
+    <inputs>
+        <conditional name="db">
+            <param name="src" type="select" label="Source for dbNSFP file">
+                <option value="softgenetics">Jpopgen dbNSFP from softgenetics</option>
+                <option value="history">from your history</option>
+            </param>
+            <when value="softgenetics">
+                <param name="softgenetics_name" type="text" value="" label="dbNSFP file name at softgenetics ftp site">
+                  <help>Download From:  ftp://dbnsfp.softgenetics.com/
+                        Enter the name of the database, e.g.:  dbNSFPv3.0c.zip
+                  </help>
+                  <validator type="regex"  message="A dbNSFP or dbscSNV .zip">(dbNSFP|dbscSNV).*[.]zip</validator>
+                </param>
+            </when>
+            <when value="history">
+                <param name="snpsiftdbnsfp" type="data" format="snpsiftdbnsfp,dbnsfp.tabular" label="A snpsift dbnsfp from your history" 
+                 help="This can can be generated by converting a tabular file set to type: dbnsfp.tabular"/>
+                <param name="db_name" type="text" value="" label="The unique name to give this dbnsfp database">
+                  <validator type="length" min="3" max="20" message="Must have between 3 and 20 chracters"/>
+                  <validator type="regex" message="No whitespace allowed">^\S*$</validator>
+                </param>
+                <param name="dbkey" type="text" value="hg19" optional="true" label="DBKEY to assign to data to this dbNSFP database" />
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+           <data name="out_file" format="data_manager_json" label="${tool.name}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="src" value="history"/>
+            <param name="snpsiftdbnsfp" value="test_nsfp.tsv" ftype="dbnsfp.tabular"/>
+            <param name="dbkey" value="hg19"/>
+            <param name="db_name" value="test_nsfp_tsv" />
+            <output name="out_file" file="test_nsfp.data_manager_json"/>
+        </test>
+    </tests>
+    <help>
+
+This tool installs dbNSFP_ databases to annotate VCF files using SnpSift_dbNSFP_
+It populates data table: snpsift_dbnsfps
+
+.. _dbNSFP: https://sites.google.com/site/jpopgen/dbNSFP
+.. _SnpSift_dbNSFP: http://snpefIf.sourceforge.net/SnpSift.html#dbNSFP 
+
+Please refer to https://sites.google.com/site/jpopgen/dbNSFP for which citations to use with specific dbNSFP database versions.
+
+    </help>
+    <citations>
+        <citation type="doi">DOI: 10.1002/humu.21517</citation>
+        <citation type="doi">DOI: 10.1002/humu.22376</citation>
+        <citation type="doi">DOI: 10.1002/humu.22932</citation>
+        <citation type="doi">doi: 10.1093/hmg/ddu733</citation>
+        <citation type="doi">doi: 10.1093/nar/gku1206</citation>
+        <citation type="doi">doi: 10.3389/fgene.2012.00035</citation>
+    </citations>
+</tool>
+