diff pi_dbspec_align.xml @ 2:77ddaee887a8 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pi_dbspec_align.xml	Fri Sep 01 03:14:54 2017 -0400
@@ -0,0 +1,77 @@
+<tool id="pi_dbspec_align" name="Align DB fractions" version="0.3">
+    <description>to resemble spectra fraction scheme</description>
+    <requirements>
+        <requirement type="package" version="3.6">python</requirement>
+	<requirement type="package" version="1.62">biopython</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+	    <![CDATA[
+	    mkdir aligned_out && 
+	    python '$__tool_directory__/align_dbspec.py' 
+	    --specnames $specnames
+	    --dbfiles 
+		#for $key in $databases.keys()
+		'$databases[$key]'
+ 		#end for
+	    --frspec '$frspec'
+	    --firstfr $firstfr
+
+	    ]]>
+    </command>
+    
+    <inputs>
+	    <param name="specnames" type="data" format="text,tabular" label="Spectra files" />
+	    <param name="databases" type="data_collection" collection_type="list" format="fasta" label="Fractionated databases" />
+      	    <param name="frspec" type="text" label="Regex to find fraction numbers in spectra file names" help="If spectra file is called myspectra_fr01b.mzML, use .*fr([0-9]+).*" >
+            <sanitizer>
+                <valid initial="string.printable">
+                    <remove value="&apos;"/>
+                </valid>
+            </sanitizer>
+	</param>
+      	    <param name="firstfr" type="integer" value="1" label="First fraction number in series" />
+    </inputs>
+    
+    <outputs>
+	<collection name="aligned_db" type="list" label="spectra-fraction-aligned DB">
+            <discover_datasets pattern="__designation__" ext="fasta" directory="aligned_out" />
+	</collection>
+    </outputs>
+    <tests>
+	    <test>
+		    <param name="specnames" value="specnames.txt" />
+		    <param name="databases">
+		    	<collection type="list">
+			    <element name="fr1" value="target_splitdb_fr1.fasta" />
+			    <element name="fr2" value="target_splitdb_fr2.fasta" />
+			    <element name="fr3" value="target_splitdb_fr3.fasta" />
+			    <element name="fr4" value="decoy_splitdb_fr1.fasta" />
+			    <element name="fr5" value="decoy_splitdb_fr2.fasta" />
+			    <element name="fr6" value="decoy_splitdb_fr3.fasta" />
+			    <element name="fr7" value="decoy_splitdb_fr1.fasta" />
+			    <element name="fr8" value="decoy_splitdb_fr2.fasta" />
+			    <element name="fr9" value="decoy_splitdb_fr3.fasta" />
+			</collection>
+			</param>
+		    <param name="frspec" value=".*c_f([0-9]+).*" />
+		    <param name="firstfr" value="1" />
+		    <output_collection name="aligned_db" type="list">
+			    <element name="spec_f01.mzML" value="target_splitdb_fr1.fasta" />
+			    <element name="spec_f02.mzML" value="target_splitdb_fr2.fasta" />
+			    <element name="spec_f03.mzML" value="target_splitdb_fr3.fasta" />
+			    <element name="spec_f03b.mzML" value="target_splitdb_fr3.fasta" />
+			    <element name="spec_f09.mzML" value="merged_twice_decoy_fr1-3.fasta" compare="sim_size" />
+			    <element name="spec_f09b.mzML" value="merged_twice_decoy_fr1-3.fasta" compare="sim_size" />
+		    </output_collection>
+	    </test>
+    </tests>
+
+    <help>
+	    Filters, pools and doubles fractionated databases with a set of identically fractionated spectra files which have been
+	    subjected to pooling and contain reruns.
+	    You may have fraction 1-10 in databases but spectra file fractions 4-7 have been pooled before loading to the MS, 
+	    and spectra fraction 2 and 8 have been reran creating fractions 2 and 2a, and 8, 8a and 8b.
+	    This tool pools FASTA databases and duplicates them where needed to line up the databases to your spectra collections.
+    </help>
+
+</tool>